WorldWideScience

Sample records for single-species population models

  1. The Bifurcation and Control of a Single-Species Fish Population Logistic Model with the Invasion of Alien Species

    OpenAIRE

    Zhang, Yi; Zhang, Qiaoling; Li, Jinghao; Zhang, Qingling

    2014-01-01

    The objective of this paper is to study systematically the bifurcation and control of a single-species fish population logistic model with the invasion of alien species based on the theory of singular system and bifurcation. It regards Spartina anglica as an invasive species, which invades the fisheries and aquaculture. Firstly, the stabilities of equilibria in this model are discussed. Moreover, the sufficient conditions for existence of the trans-critical bifurcation and the singularity ind...

  2. The Bifurcation and Control of a Single-Species Fish Population Logistic Model with the Invasion of Alien Species

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2014-01-01

    Full Text Available The objective of this paper is to study systematically the bifurcation and control of a single-species fish population logistic model with the invasion of alien species based on the theory of singular system and bifurcation. It regards Spartina anglica as an invasive species, which invades the fisheries and aquaculture. Firstly, the stabilities of equilibria in this model are discussed. Moreover, the sufficient conditions for existence of the trans-critical bifurcation and the singularity induced bifurcation are obtained. Secondly, the state feedback controller is designed to eliminate the unexpected singularity induced bifurcation by combining harvested effort with the purification capacity. It obviously inhibits the switch of population and makes the system stable. Finally, the numerical simulation is proposed to show the practical significance of the bifurcation and control from the biological point of view.

  3. A comparison of fisheries biological reference points estimated from temperature-specific multi-species and single-species climate-enhanced stock assessment models

    Science.gov (United States)

    Holsman, Kirstin K.; Ianelli, James; Aydin, Kerim; Punt, André E.; Moffitt, Elizabeth A.

    2016-12-01

    Multi-species statistical catch at age models (MSCAA) can quantify interacting effects of climate and fisheries harvest on species populations, and evaluate management trade-offs for fisheries that target several species in a food web. We modified an existing MSCAA model to include temperature-specific growth and predation rates and applied the modified model to three fish species, walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus) and arrowtooth flounder (Atheresthes stomias), from the eastern Bering Sea (USA). We fit the model to data from 1979 through 2012, with and without trophic interactions and temperature effects, and use projections to derive single- and multi-species biological reference points (BRP and MBRP, respectively) for fisheries management. The multi-species model achieved a higher over-all goodness of fit to the data (i.e. lower negative log-likelihood) for pollock and Pacific cod. Variability from water temperature typically resulted in 5-15% changes in spawning, survey, and total biomasses, but did not strongly impact recruitment estimates or mortality. Despite this, inclusion of temperature in projections did have a strong effect on BRPs, including recommended yield, which were higher in single-species models for Pacific cod and arrowtooth flounder that included temperature compared to the same models without temperature effects. While the temperature-driven multi-species model resulted in higher yield MBPRs for arrowtooth flounder than the same model without temperature, we did not observe the same patterns in multi-species models for pollock and Pacific cod, where variability between harvest scenarios and predation greatly exceeded temperature-driven variability in yield MBRPs. Annual predation on juvenile pollock (primarily cannibalism) in the multi-species model was 2-5 times the annual harvest of adult fish in the system, thus predation represents a strong control on population dynamics that exceeds temperature

  4. The reverse effects of random perturbation on discrete systems for single and multiple population models

    International Nuclear Information System (INIS)

    Kang, Li; Tang, Sanyi

    2016-01-01

    Highlights: • The discrete single species and multiple species models with random perturbation are proposed. • The complex dynamics and interesting bifurcation behavior have been investigated. • The reverse effects of random perturbation on discrete systems have been discussed and revealed. • The main results can be applied for pest control and resources management. - Abstract: The natural species are likely to present several interesting and complex phenomena under random perturbations, which have been confirmed by simple mathematical models. The important questions are: how the random perturbations influence the dynamics of the discrete population models with multiple steady states or multiple species interactions? and is there any different effects for single species and multiple species models with random perturbation? To address those interesting questions, we have proposed the discrete single species model with two stable equilibria and the host-parasitoid model with Holling type functional response functions to address how the random perturbation affects the dynamics. The main results indicate that the random perturbation does not change the number of blurred orbits of the single species model with two stable steady states compared with results for the classical Ricker model with same random perturbation, but it can strength the stability. However, extensive numerical investigations depict that the random perturbation does not influence the complexities of the host-parasitoid models compared with the results for the models without perturbation, while it does increase the period of periodic orbits doubly. All those confirm that the random perturbation has a reverse effect on the dynamics of the discrete single and multiple population models, which could be applied in reality including pest control and resources management.

  5. Estimating Effects of Species Interactions on Populations of Endangered Species.

    Science.gov (United States)

    Roth, Tobias; Bühler, Christoph; Amrhein, Valentin

    2016-04-01

    Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

  6. The effect of seasonal harvesting on a single-species discrete population model with stage structure and birth pulses

    International Nuclear Information System (INIS)

    Gao Shujing; Chen Lansun

    2005-01-01

    In this paper, we propose an exploited single-species discrete model with stage structure for the dynamics in a fish population for which births occur in a single pulse once per time period. Using the stroboscopic map, we obtain an exact cycle of the system, and obtain the threshold conditions for its stability. Bifurcation diagrams are constructed with the birth rate as the bifurcation parameter, and these are observed to display complex dynamic behaviors, including chaotic bands with period windows, pitch-fork and tangent bifurcation. This suggests that birth pulse provides a natural period or cyclicity that makes the dynamical behavior more complex. Moreover, we show that the timing of harvesting has a strong impact on the persistence of the fish population, on the volume of mature fish stock and on the maximum annual-sustainable yield. An interesting result is obtained that, after the birth pulse, the earlier culling the mature fish, the larger harvest can tolerate

  7. Persistence and extinction of a stochastic single-species population model in a polluted environment with impulsive toxicant input

    Directory of Open Access Journals (Sweden)

    Meng Liu

    2013-10-01

    Full Text Available A stochastic single-species population system in a polluted environment with impulsive toxicant input is proposed and studied. Sufficient conditions for extinction, non-persistence in the mean, strong persistence in the mean and stochastic permanence of the population are established. The threshold between strong persistence in the mean and extinction is obtained. Some simulation figures are introduced to illustrate the main results.

  8. Richards-like two species population dynamics model.

    Science.gov (United States)

    Ribeiro, Fabiano; Cabella, Brenno Caetano Troca; Martinez, Alexandre Souto

    2014-12-01

    The two-species population dynamics model is the simplest paradigm of inter- and intra-species interaction. Here, we present a generalized Lotka-Volterra model with intraspecific competition, which retrieves as particular cases, some well-known models. The generalization parameter is related to the species habitat dimensionality and their interaction range. Contrary to standard models, the species coupling parameters are general, not restricted to non-negative values. Therefore, they may represent different ecological regimes, which are derived from the asymptotic solution stability analysis and are represented in a phase diagram. In this diagram, we have identified a forbidden region in the mutualism regime, and a survival/extinction transition with dependence on initial conditions for the competition regime. Also, we shed light on two types of predation and competition: weak, if there are species coexistence, or strong, if at least one species is extinguished.

  9. Near infra-red spectroscopy quantitative modelling of bivalve protein, lipid and glycogen composition using single-species versus multi-species calibration and validation sets

    Science.gov (United States)

    Bartlett, Jill K.; Maher, William A.; Purss, Matthew B. J.

    2018-03-01

    Near infrared spectroscopy (NIRS) quantitative modelling was used to measure the protein, lipid and glycogen composition of five marine bivalve species (Saccostrea glomerata, Ostrea angasi, Crassostrea gigas, Mytilus galloprovincialis and Anadara trapezia) from multiple locations and seasons. Predictive models were produced for each component using individual species and aggregated sample populations for the three oyster species (S. glomerata, O. angasi and C. gigas) and for all five bivalve species. Whole animal tissues were freeze dried, ground to > 20 μm and scanned by NIRS. Protein, lipid and glycogen composition were determined by traditional chemical analyses and calibration models developed to allow rapid NIRS-measurement of these components in the five bivalve species. Calibration modelling was performed using wavelet selection, genetic algorithms and partial least squares analysis. Model quality was assessed using RPIQ and RMESP. For protein composition, single species model results had RPIQ values between 2.4 and 3.5 and RMSEP between 8.6 and 18%, the three oyster model had an RPIQ of 2.6 and an RMSEP of 10.8% and the five bivalve species had an RPIQ of 3.6 and RMSEP of 8.7% respectively. For lipid composition, single species models achieved RPIQ values between 2.9 and 5.3 with RMSEP between 9.1 and 11.2%, the oyster model had an RPIQ of 3.6 and RMSEP of 6.8 and the five bivalve model had an RPIQ of 5.2 and RMSEP of 6.8% respectively. For glycogen composition, the single species models had RPIQs between 3.8 and 18.9 with RMSEP between 3.5 and 9.2%, the oyster model had an RPIQ of 5.5 and RMSEP of 7.1% and the five bivalve model had an RPIQ of 4 and RMSEP of 7.6% respectively. Comparison between individual species models and aggregated models for three oyster species and five bivalve species for each component indicate that aggregating data from like species produces high quality models with robust and reliable quantitative application. The benefit of

  10. On the apllication of single specie dynamic population model | Iguda ...

    African Journals Online (AJOL)

    The Method of mathematical models of Malthus and Verhults were applied on ten years data collected from Magaram Poultry Farm to determine the nature of population growth, population decay or constant ... Keywords: Birth rate, sustainable population, overcrowding, harvesting, independent t-test and one way Anova.

  11. Approximate probabilistic cellular automata for the dynamics of single-species populations under discrete logisticlike growth with and without weak Allee effects.

    Science.gov (United States)

    Mendonça, J Ricardo G; Gevorgyan, Yeva

    2017-05-01

    We investigate one-dimensional elementary probabilistic cellular automata (PCA) whose dynamics in first-order mean-field approximation yields discrete logisticlike growth models for a single-species unstructured population with nonoverlapping generations. Beginning with a general six-parameter model, we find constraints on the transition probabilities of the PCA that guarantee that the ensuing approximations make sense in terms of population dynamics and classify the valid combinations thereof. Several possible models display a negative cubic term that can be interpreted as a weak Allee factor. We also investigate the conditions under which a one-parameter PCA derived from the more general six-parameter model can generate valid population growth dynamics. Numerical simulations illustrate the behavior of some of the PCA found.

  12. Persistence and extinction of a single-species population system in a polluted environment with random perturbations and impulsive toxicant input

    International Nuclear Information System (INIS)

    Liu Meng; Wang Ke

    2012-01-01

    Highlights: ► Random population model with pulse toxicant input in polluted environments. ► Threshold between persistence and extinction is obtained. ► Different random noises have different effects on the persistence of the population. ► Impulsive period plays a key role in determining persistence of the population. ► Simulation figures support the analytical findings. - Abstract: Taking both white noises and colored noises into account, a stochastic single-species model with Markov switching and impulsive toxicant input in a polluted environment is proposed and investigated. Sufficient conditions for extinction, non-persistence in the mean, weak persistence and stochastic permanence are established. The threshold between weak persistence and extinction is obtained. Some simulation figures are introduced to illustrate the main results.

  13. Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

    Directory of Open Access Journals (Sweden)

    Conor P. McGowan

    2017-10-01

    Full Text Available Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises in transparent and explicit ways tailored to support decision making processes related to endangered species.

  14. Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

    Science.gov (United States)

    McGowan, Conor P.; Allan, Nathan; Servoss, Jeff; Hedwall, Shaula J.; Wooldridge, Brian

    2017-01-01

    Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises) in transparent and explicit ways tailored to support decision making processes related to endangered species.

  15. Addressing potential local adaptation in species distribution models: implications for conservation under climate change

    Science.gov (United States)

    Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason D. K.; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C.; Hellmann, Jessica J.

    2016-01-01

    Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

  16. A structurally based analytic model of growth and biomass dynamics in single species stands of conifers

    Science.gov (United States)

    Robin J. Tausch

    2015-01-01

    A theoretically based analytic model of plant growth in single species conifer communities based on the species fully occupying a site and fully using the site resources is introduced. Model derivations result in a single equation simultaneously describes changes over both, different site conditions (or resources available), and over time for each variable for each...

  17. Deconstructing stem cell population heterogeneity: Single-cell analysis and modeling approaches

    Science.gov (United States)

    Wu, Jincheng; Tzanakakis, Emmanuel S.

    2014-01-01

    Isogenic stem cell populations display cell-to-cell variations in a multitude of attributes including gene or protein expression, epigenetic state, morphology, proliferation and proclivity for differentiation. The origins of the observed heterogeneity and its roles in the maintenance of pluripotency and the lineage specification of stem cells remain unclear. Addressing pertinent questions will require the employment of single-cell analysis methods as traditional cell biochemical and biomolecular assays yield mostly population-average data. In addition to time-lapse microscopy and flow cytometry, recent advances in single-cell genomic, transcriptomic and proteomic profiling are reviewed. The application of multiple displacement amplification, next generation sequencing, mass cytometry and spectrometry to stem cell systems is expected to provide a wealth of information affording unprecedented levels of multiparametric characterization of cell ensembles under defined conditions promoting pluripotency or commitment. Establishing connections between single-cell analysis information and the observed phenotypes will also require suitable mathematical models. Stem cell self-renewal and differentiation are orchestrated by the coordinated regulation of subcellular, intercellular and niche-wide processes spanning multiple time scales. Here, we discuss different modeling approaches and challenges arising from their application to stem cell populations. Integrating single-cell analysis with computational methods will fill gaps in our knowledge about the functions of heterogeneity in stem cell physiology. This combination will also aid the rational design of efficient differentiation and reprogramming strategies as well as bioprocesses for the production of clinically valuable stem cell derivatives. PMID:24035899

  18. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    Science.gov (United States)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

  19. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.

    Directory of Open Access Journals (Sweden)

    Artémis Llamosi

    2016-02-01

    Full Text Available Significant cell-to-cell heterogeneity is ubiquitously observed in isogenic cell populations. Consequently, parameters of models of intracellular processes, usually fitted to population-averaged data, should rather be fitted to individual cells to obtain a population of models of similar but non-identical individuals. Here, we propose a quantitative modeling framework that attributes specific parameter values to single cells for a standard model of gene expression. We combine high quality single-cell measurements of the response of yeast cells to repeated hyperosmotic shocks and state-of-the-art statistical inference approaches for mixed-effects models to infer multidimensional parameter distributions describing the population, and then derive specific parameters for individual cells. The analysis of single-cell parameters shows that single-cell identity (e.g. gene expression dynamics, cell size, growth rate, mother-daughter relationships is, at least partially, captured by the parameter values of gene expression models (e.g. rates of transcription, translation and degradation. Our approach shows how to use the rich information contained into longitudinal single-cell data to infer parameters that can faithfully represent single-cell identity.

  20. Maintaining animal assemblages through single-species management: the case of threatened caribou in boreal forest.

    Science.gov (United States)

    Bichet, Orphé; Dupuch, Angélique; Hébert, Christian; Le Borgne, Hélène Le; Fortin, Daniel

    2016-03-01

    With the intensification of human activities, preserving animal populations is a contemporary challenge of critical importance. In this context, the umbrella species concept is appealing because preserving a single species should result in the protection of multiple co-occurring species. Practitioners, though, face the task of having to find suitable umbrellas to develop single-species management guidelines. In North America, boreal forests must be managed to facilitate the recovery of the threatened boreal caribou (Rangifer tarandus). Yet, the effect of caribou conservation on co-occurring animal species remains poorly documented. We tested if boreal caribou can constitute an effective umbrella for boreal fauna. Birds, small mammals, and insects were sampled along gradients of post-harvest and post-fire forest succession. Predictive models of occupancy were developed from the responses of 95 species to characteristics of forest stands and their surroundings. We then assessed the similarity of species occupancy expected between simulated harvested landscapes and a 90 000-km2 uncut landscape. Managed landscapes were simulated based on three levels of disturbance, two timber-harvest rotation cycles, and dispersed or aggregated cut-blocks. We found that management guidelines that were more likely to maintain caribou populations should also better preserve animal assemblages. Relative to fragmentation or harvest cycle, we detected a stronger effect of habitat loss on species assemblages. Disturbing 22%, 35%, and 45% of the landscape should result, respectively, in 80%, 60%, and 40% probability for caribou populations to be sustainable; in turn, this should result in regional species assemblages with Jaccard similarity indices of 0.86, 0.79, and 0.74, respectively, relative to the uncut landscape. Our study thus demonstrates the value of single-species management for animal conservation. Our quantitative approach allows for the evaluation of management guidelines prior

  1. Two-species occupancy modeling accounting for species misidentification and nondetection

    Science.gov (United States)

    Chambert, Thierry; Grant, Evan H. Campbell; Miller, David A. W.; Nichols, James; Mulder, Kevin P.; Brand, Adrianne B,

    2018-01-01

    1. In occupancy studies, species misidentification can lead to false positive detections, which can cause severe estimator biases. Currently, all models that account for false positive errors only consider omnibus sources of false detections and are limited to single species occupancy. 2. However, false detections for a given species often occur because of the misidentification with another, closely-related species. To exploit this explicit source of false positive detection error, we develop a two-species occupancy model that accounts for misidentifications between two species of interest. As with other false positive models, identifiability is greatly improved by the availability of unambiguous detections at a subset of site-occasions. Here, we consider the case where some of the field observations can be confirmed using laboratory or other independent identification methods (“confirmatory data”). 3. We performed three simulation studies to (1) assess the model’s performance under various realistic scenarios, (2) investigate the influence of the proportion of confirmatory data on estimator accuracy, and (3) compare the performance of this two-species model with that of the single-species false positive model. The model shows good performance under all scenarios, even when only small proportions of detections are confirmed (e.g., 5%). It also clearly outperforms the single-species model.

  2. Confronting species distribution model predictions with species functional traits.

    Science.gov (United States)

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  3. A nonlocal and periodic reaction-diffusion-advection model of a single phytoplankton species.

    Science.gov (United States)

    Peng, Rui; Zhao, Xiao-Qiang

    2016-02-01

    In this article, we are concerned with a nonlocal reaction-diffusion-advection model which describes the evolution of a single phytoplankton species in a eutrophic vertical water column where the species relies solely on light for its metabolism. The new feature of our modeling equation lies in that the incident light intensity and the death rate are assumed to be time periodic with a common period. We first establish a threshold type result on the global dynamics of this model in terms of the basic reproduction number R0. Then we derive various characterizations of R0 with respect to the vertical turbulent diffusion rate, the sinking or buoyant rate and the water column depth, respectively, which in turn give rather precise conditions to determine whether the phytoplankton persist or become extinct. Our theoretical results not only extend the existing ones for the time-independent case, but also reveal new interesting effects of the modeling parameters and the time-periodic heterogeneous environment on persistence and extinction of the phytoplankton species, and thereby suggest important implications for phytoplankton growth control.

  4. Using species abundance distribution models and diversity indices for biogeographical analyses

    Science.gov (United States)

    Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.

    2016-01-01

    We examine whether Species Abundance Distribution models (SADs) and diversity indices can describe how species colonization status influences species community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic species restricted to only one island, should be represented by few rare species and consequently have abundance patterns that differ from those of more widespread species. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the species into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-abundance plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly abundant species and a lack of rare species, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted species; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for

  5. Conservation biology for suites of species: Demographic modeling for Pacific island kingfishers

    Science.gov (United States)

    Kesler, D.C.; Haig, S.M.

    2007-01-01

    Conservation practitioners frequently extrapolate data from single-species investigations when managing critically endangered populations. However, few researchers initiate work with the intent of making findings useful to conservation efforts for other species. We presented and explored the concept of conducting conservation-oriented research for suites of geographically separated populations with similar natural histories, resource needs, and extinction threats. An example was provided in the form of an investigation into the population demography of endangered Micronesian kingfishers (Todiramphus cinnamominus). We provided the first demographic parameter estimates for any of the 12 endangered Pacific Todiramphus species, and used results to develop a population projection matrix model for management throughout the insular Pacific. Further, we used the model for elasticity and simulation analyses with demographic values that randomly varied across ranges that might characterize congener populations. Results from elasticity and simulation analyses indicated that changes in breeding adult survival exerted the greatest magnitude of influence on population dynamics. However, changes in nestling survival were more consistently correlated with population dynamics as demographic rates were randomly altered. We concluded that conservation practitioners working with endangered Pacific kingfishers should primarily focus efforts on factors affecting nestling and breeder survival, and secondarily address fledgling juveniles and helpers. Further, we described how the generalized base model might be changed to focus on individual populations and discussed the potential application of multi-species models to other conservation situations. ?? 2007 Elsevier Ltd. All rights reserved.

  6. Addressing challenges in single species assessments via a simple state-space assessment model

    DEFF Research Database (Denmark)

    Nielsen, Anders

    Single-species and age-structured fish stock assessments still remains the main tool for managing fish stocks. A simple state-space assessment model is presented as an alternative to (semi) deterministic procedures and the full parametric statistical catch at age models. It offers a solution...... to some of the key challenges of these models. Compared to the deterministic procedures it solves a list of problems originating from falsely assuming that age classified catches are known without errors and allows quantification of uncertainties of estimated quantities of interest. Compared to full...

  7. Persistence and extinction of a stochastic single-species model under regime switching in a polluted environment II.

    Science.gov (United States)

    Liu, Meng; Wang, Ke

    2010-12-07

    This is a continuation of our paper [Liu, M., Wang, K., 2010. Persistence and extinction of a stochastic single-species model under regime switching in a polluted environment, J. Theor. Biol. 264, 934-944]. Taking both white noise and colored noise into account, a stochastic single-species model under regime switching in a polluted environment is studied. Sufficient conditions for extinction, stochastic nonpersistence in the mean, stochastic weak persistence and stochastic permanence are established. The threshold between stochastic weak persistence and extinction is obtained. The results show that a different type of noise has a different effect on the survival results. Copyright © 2010 Elsevier Ltd. All rights reserved.

  8. Genomic prediction in a nuclear population of layers using single-step models.

    Science.gov (United States)

    Yan, Yiyuan; Wu, Guiqin; Liu, Aiqiao; Sun, Congjiao; Han, Wenpeng; Li, Guangqi; Yang, Ning

    2018-02-01

    Single-step genomic prediction method has been proposed to improve the accuracy of genomic prediction by incorporating information of both genotyped and ungenotyped animals. The objective of this study is to compare the prediction performance of single-step model with a 2-step models and the pedigree-based models in a nuclear population of layers. A total of 1,344 chickens across 4 generations were genotyped by a 600 K SNP chip. Four traits were analyzed, i.e., body weight at 28 wk (BW28), egg weight at 28 wk (EW28), laying rate at 38 wk (LR38), and Haugh unit at 36 wk (HU36). In predicting offsprings, individuals from generation 1 to 3 were used as training data and females from generation 4 were used as validation set. The accuracies of predicted breeding values by pedigree BLUP (PBLUP), genomic BLUP (GBLUP), SSGBLUP and single-step blending (SSBlending) were compared for both genotyped and ungenotyped individuals. For genotyped females, GBLUP performed no better than PBLUP because of the small size of training data, while the 2 single-step models predicted more accurately than the PBLUP model. The average predictive ability of SSGBLUP and SSBlending were 16.0% and 10.8% higher than the PBLUP model across traits, respectively. Furthermore, the predictive abilities for ungenotyped individuals were also enhanced. The average improvements of prediction abilities were 5.9% and 1.5% for SSGBLUP and SSBlending model, respectively. It was concluded that single-step models, especially the SSGBLUP model, can yield more accurate prediction of genetic merits and are preferable for practical implementation of genomic selection in layers. © 2017 Poultry Science Association Inc.

  9. Assessing three fish species ecological status in Colorado River, Grand Canyon based on physical habitat and population models.

    Science.gov (United States)

    Yao, Weiwei; Chen, Yuansheng

    2018-04-01

    Colorado River is a unique ecosystem and provides important ecological services such as habitat for fish species as well as water power energy supplies. River management for this ecosystem requires assessment and decision support tools for fish which involves protecting, restoring as well as forecasting of future conditions. In this paper, a habitat and population model was developed and used to determine the levels of fish habitat suitability and population density in Colorado River between Lees Ferry and Lake Mead. The short term target fish populations are also predicted based on native fish recovery strategy. This model has been developed by combining hydrodynamics, heat transfer and sediment transport models with a habitat suitability index model and then coupling with habitat model into life stage population model. The fish were divided into four life stages according to the fish length. Three most abundant and typical native and non-native fish were selected as target species, which are rainbow trout (Oncorhynchus mykiss), brown trout (Salmo trutta) and flannelmouth sucker (Catostomus latipinnis). Flow velocity, water depth, water temperature and substrates were used as the suitability indicators in habitat model and overall suitability index (OSI) as well as weight usable area (WUA) was used as an indicator in population model. A comparison was made between simulated fish population alteration and surveyed fish number fluctuation during 2000 to 2009. The application of this habitat and population model indicates that this model can be accurate present habitat situation and targets fish population dynamics of in the study areas. The analysis also indicates the flannelmouth sucker population will steadily increase while the rainbow trout will decrease based on the native fish recovery scheme. Copyright © 2018. Published by Elsevier Inc.

  10. Developing population models with data from marked individuals

    Science.gov (United States)

    Hae Yeong Ryu,; Kevin T. Shoemaker,; Eva Kneip,; Anna Pidgeon,; Patricia Heglund,; Brooke Bateman,; Thogmartin, Wayne E.; Reşit Akçakaya,

    2016-01-01

    Population viability analysis (PVA) is a powerful tool for biodiversity assessments, but its use has been limited because of the requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. Developing a fully specified population model from commonly available data sources – notably, mark–recapture studies – remains complicated due to lack of practical methods for estimating fecundity, true survival (as opposed to apparent survival), natural temporal variability in both survival and fecundity, density-dependence in the demographic parameters, and uncertainty in model parameters. We present a general method that estimates all the key parameters required to specify a stochastic, matrix-based population model, constructed using a long-term mark–recapture dataset. Unlike standard mark–recapture analyses, our approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. Furthermore, our method includes a formal quantification of parameter uncertainty for global (multivariate) sensitivity analysis. We apply this approach to 9 bird species and demonstrate the feasibility of using data from the Monitoring Avian Productivity and Survivorship (MAPS) program. Bias-correction factors for raw estimates of survival and fecundity derived from mark–recapture data (apparent survival and juvenile:adult ratio, respectively) were non-negligible, and corrected parameters were generally more biologically reasonable than their uncorrected counterparts. Our method allows the development of fully specified stochastic population models using a single, widely available data source, substantially reducing the barriers that have until now limited the widespread application of PVA. This method

  11. Demography of a reintroduced population: moving toward management models for an endangered species, the whooping crane

    Science.gov (United States)

    Servanty, Sabrina; Converse, Sarah J.; Bailey, Larissa L.

    2014-01-01

    The reintroduction of threatened and endangered species is now a common method for reestablishing populations. Typically, a fundamental objective of reintroduction is to establish a self-sustaining population. Estimation of demographic parameters in reintroduced populations is critical, as these estimates serve multiple purposes. First, they support evaluation of progress toward the fundamental objective via construction of population viability analyses (PVAs) to predict metrics such as probability of persistence. Second, PVAs can be expanded to support evaluation of management actions, via management modeling. Third, the estimates themselves can support evaluation of the demographic performance of the reintroduced population, e.g., via comparison with wild populations. For each of these purposes, thorough treatment of uncertainties in the estimates is critical. Recently developed statistical methods - namely, hierarchical Bayesian implementations of state-space models - allow for effective integration of different types of uncertainty in estimation. We undertook a demographic estimation effort for a reintroduced population of endangered whooping cranes with the purpose of ultimately developing a Bayesian PVA for determining progress toward establishing a self-sustaining population, and for evaluating potential management actions via a Bayesian PVA-based management model. We evaluated individual and temporal variation in demographic parameters based upon a multi-state mark-recapture model. We found that survival was relatively high across time and varied little by sex. There was some indication that survival varied by release method. Survival was similar to that observed in the wild population. Although overall reproduction in this reintroduced population is poor, birds formed social pairs when relatively young, and once a bird was in a social pair, it had a nearly 50% chance of nesting the following breeding season. Also, once a bird had nested, it had a high

  12. Matrix population models from 20 studies of perennial plant populations

    Science.gov (United States)

    Ellis, Martha M.; Williams, Jennifer L.; Lesica, Peter; Bell, Timothy J.; Bierzychudek, Paulette; Bowles, Marlin; Crone, Elizabeth E.; Doak, Daniel F.; Ehrlen, Johan; Ellis-Adam, Albertine; McEachern, Kathryn; Ganesan, Rengaian; Latham, Penelope; Luijten, Sheila; Kaye, Thomas N.; Knight, Tiffany M.; Menges, Eric S.; Morris, William F.; den Nijs, Hans; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F.; Shelly, J. Stephen; Stanley, Amanda; Thorpe, Andrea; Tamara, Ticktin; Valverde, Teresa; Weekley, Carl W.

    2012-01-01

    Demographic transition matrices are one of the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long-term demographic monitoring. These data were assembled as part of the 'Testing Matrix Models' working group through the National Center for Ecological Analysis and Synthesis (NCEAS). In sum, these data represent 82 populations with >460 total population-years of data. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics.

  13. Modelling the impact of toxic and disturbance stress on white-tailed eagle (Haliaeetus albicilla) populations.

    Science.gov (United States)

    Korsman, John C; Schipper, Aafke M; Lenders, H J Rob; Foppen, Ruud P B; Hendriks, A Jan

    2012-01-01

    Several studies have related breeding success and survival of sea eagles to toxic or non-toxic stress separately. In the present investigation, we analysed single and combined impacts of both toxic and disturbance stress on populations of white-tailed eagle (Haliaeetus albicilla), using an analytical single-species model. Chemical and eco(toxico)logical data reported from laboratory and field studies were used to parameterise and validate the model. The model was applied to assess the impact of ∑PCB, DDE and disturbance stress on the white-tailed eagle population in The Netherlands. Disturbance stress was incorporated through a 1.6% reduction in survival and a 10-50% reduction in reproduction. ∑PCB contamination from 1950 up to 1987 was found to be too high to allow the return of white-tailed eagle as a breeding species in that period. ∑PCB and population trends simulated for 2006-2050 suggest that future population growth is still reduced. Disturbance stress resulted in a reduced population development. The combination of both toxic and disturbance stress varied from a slower population development to a catastrophical reduction in population size, where the main cause was attributed to the reduction in reproduction of 50%. Application of the model was restricted by the current lack of quantitative dose-response relationships between non-toxic stress and survival and reproduction. Nevertheless, the model provides a first step towards integrating and quantifying the impacts of multiple stressors on white-tailed eagle populations.

  14. Differing effects of attention in single-units and populations are well predicted by heterogeneous tuning and the normalization model of attention.

    Science.gov (United States)

    Hara, Yuko; Pestilli, Franco; Gardner, Justin L

    2014-01-01

    Single-unit measurements have reported many different effects of attention on contrast-response (e.g., contrast-gain, response-gain, additive-offset dependent on visibility), while functional imaging measurements have more uniformly reported increases in response across all contrasts (additive-offset). The normalization model of attention elegantly predicts the diversity of effects of attention reported in single-units well-tuned to the stimulus, but what predictions does it make for more realistic populations of neurons with heterogeneous tuning? Are predictions in accordance with population-scale measurements? We used functional imaging data from humans to determine a realistic ratio of attention-field to stimulus-drive size (a key parameter for the model) and predicted effects of attention in a population of model neurons with heterogeneous tuning. We found that within the population, neurons well-tuned to the stimulus showed a response-gain effect, while less-well-tuned neurons showed a contrast-gain effect. Averaged across the population, these disparate effects of attention gave rise to additive-offsets in contrast-response, similar to reports in human functional imaging as well as population averages of single-units. Differences in predictions for single-units and populations were observed across a wide range of model parameters (ratios of attention-field to stimulus-drive size and the amount of baseline response modifiable by attention), offering an explanation for disparity in physiological reports. Thus, by accounting for heterogeneity in tuning of realistic neuronal populations, the normalization model of attention can not only predict responses of well-tuned neurons, but also the activity of large populations of neurons. More generally, computational models can unify physiological findings across different scales of measurement, and make links to behavior, but only if factors such as heterogeneous tuning within a population are properly accounted for.

  15. Integrating count and detection–nondetection data to model population dynamics

    Science.gov (United States)

    Zipkin, Elise F.; Rossman, Sam; Yackulic, Charles B.; Wiens, David; Thorson, James T.; Davis, Raymond J.; Grant, Evan H. Campbell

    2017-01-01

    There is increasing need for methods that integrate multiple data types into a single analytical framework as the spatial and temporal scale of ecological research expands. Current work on this topic primarily focuses on combining capture–recapture data from marked individuals with other data types into integrated population models. Yet, studies of species distributions and trends often rely on data from unmarked individuals across broad scales where local abundance and environmental variables may vary. We present a modeling framework for integrating detection–nondetection and count data into a single analysis to estimate population dynamics, abundance, and individual detection probabilities during sampling. Our dynamic population model assumes that site-specific abundance can change over time according to survival of individuals and gains through reproduction and immigration. The observation process for each data type is modeled by assuming that every individual present at a site has an equal probability of being detected during sampling processes. We examine our modeling approach through a series of simulations illustrating the relative value of count vs. detection–nondetection data under a variety of parameter values and survey configurations. We also provide an empirical example of the model by combining long-term detection–nondetection data (1995–2014) with newly collected count data (2015–2016) from a growing population of Barred Owl (Strix varia) in the Pacific Northwest to examine the factors influencing population abundance over time. Our model provides a foundation for incorporating unmarked data within a single framework, even in cases where sampling processes yield different detection probabilities. This approach will be useful for survey design and to researchers interested in incorporating historical or citizen science data into analyses focused on understanding how demographic rates drive population abundance.

  16. Persistence and extinction of a stochastic single-specie model under regime switching in a polluted environment.

    Science.gov (United States)

    Liu, Meng; Wang, Ke

    2010-06-07

    A new single-species model disturbed by both white noise and colored noise in a polluted environment is developed and analyzed. Sufficient criteria for extinction, stochastic nonpersistence in the mean, stochastic weak persistence in the mean, stochastic strong persistence in the mean and stochastic permanence of the species are established. The threshold between stochastic weak persistence in the mean and extinction is obtained. The results show that both white and colored environmental noises have sufficient effect to the survival results. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  17. Species abundance distributions in neutral models with immigration or mutation and general lifetimes.

    Science.gov (United States)

    Lambert, Amaury

    2011-07-01

    We consider a general, neutral, dynamical model of biodiversity. Individuals have i.i.d. lifetime durations, which are not necessarily exponentially distributed, and each individual gives birth independently at constant rate λ. Thus, the population size is a homogeneous, binary Crump-Mode-Jagers process (which is not necessarily a Markov process). We assume that types are clonally inherited. We consider two classes of speciation models in this setting. In the immigration model, new individuals of an entirely new species singly enter the population at constant rate μ (e.g., from the mainland into the island). In the mutation model, each individual independently experiences point mutations in its germ line, at constant rate θ. We are interested in the species abundance distribution, i.e., in the numbers, denoted I(n)(k) in the immigration model and A(n)(k) in the mutation model, of species represented by k individuals, k = 1, 2, . . . , n, when there are n individuals in the total population. In the immigration model, we prove that the numbers (I(t)(k); k ≥ 1) of species represented by k individuals at time t, are independent Poisson variables with parameters as in Fisher's log-series. When conditioning on the total size of the population to equal n, this results in species abundance distributions given by Ewens' sampling formula. In particular, I(n)(k) converges as n → ∞ to a Poisson r.v. with mean γ/k, where γ : = μ/λ. In the mutation model, as n → ∞, we obtain the almost sure convergence of n (-1) A(n)(k) to a nonrandom explicit constant. In the case of a critical, linear birth-death process, this constant is given by Fisher's log-series, namely n(-1) A(n)(k) converges to α(k)/k, where α : = λ/(λ + θ). In both models, the abundances of the most abundant species are briefly discussed.

  18. General two-species interacting Lotka-Volterra system: Population dynamics and wave propagation

    Science.gov (United States)

    Zhu, Haoqi; Wang, Mao-Xiang; Lai, Pik-Yin

    2018-05-01

    The population dynamics of two interacting species modeled by the Lotka-Volterra (LV) model with general parameters that can promote or suppress the other species is studied. It is found that the properties of the two species' isoclines determine the interaction of species, leading to six regimes in the phase diagram of interspecies interaction; i.e., there are six different interspecific relationships described by the LV model. Four regimes allow for nontrivial species coexistence, among which it is found that three of them are stable, namely, weak competition, mutualism, and predator-prey scenarios can lead to win-win coexistence situations. The Lyapunov function for general nontrivial two-species coexistence is also constructed. Furthermore, in the presence of spatial diffusion of the species, the dynamics can lead to steady wavefront propagation and can alter the population map. Propagating wavefront solutions in one dimension are investigated analytically and by numerical solutions. The steady wavefront speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. In addition to the inter- and intraspecific interaction parameters, the intrinsic speed parameters of each species play a decisive role in species populations and wave properties. In some regimes, both species can copropagate with the same wave speeds in a finite range of parameters. Our results are further discussed in the light of possible biological relevance and ecological implications.

  19. Assessing environmental attributes and effects of climate change on Sphagnum peatland distributions in North America using single- and multi-species models.

    Science.gov (United States)

    Oke, Tobi A; Hager, Heather A

    2017-01-01

    The fate of Northern peatlands under climate change is important because of their contribution to global carbon (C) storage. Peatlands are maintained via greater plant productivity (especially of Sphagnum species) than decomposition, and the processes involved are strongly mediated by climate. Although some studies predict that warming will relax constraints on decomposition, leading to decreased C sequestration, others predict increases in productivity and thus increases in C sequestration. We explored the lack of congruence between these predictions using single-species and integrated species distribution models as proxies for understanding the environmental correlates of North American Sphagnum peatland occurrence and how projected changes to the environment might influence these peatlands under climate change. Using Maximum entropy and BIOMOD modelling platforms, we generated single and integrated species distribution models for four common Sphagnum species in North America under current climate and a 2050 climate scenario projected by three general circulation models. We evaluated the environmental correlates of the models and explored the disparities in niche breadth, niche overlap, and climate suitability among current and future models. The models consistently show that Sphagnum peatland distribution is influenced by the balance between soil moisture deficit and temperature of the driest quarter-year. The models identify the east and west coasts of North America as the core climate space for Sphagnum peatland distribution. The models show that, at least in the immediate future, the area of suitable climate for Sphagnum peatland could expand. This result suggests that projected warming would be balanced effectively by the anticipated increase in precipitation, which would increase Sphagnum productivity.

  20. Dynamics of radioecological and genetic processes in populations of mammalian model species at contamination of ecosystems

    International Nuclear Information System (INIS)

    Ryabokon', N.I.; Goncharova, R.I.

    2008-01-01

    A short review of data on the time course of radiobiological and genetic processes in natural populations of mammalian model species inhabiting radiocontaminated ecosystems over many generations is presented here. The described time-courses of biological end-points in these populations do not reflect the time course of the whole-body dose rates, but do the outcome of multiple processes, including the direct response to individual irradiation, the transgeneration transmission and accumulation of induced damages and the development of adaptation. (authors)

  1. Population genetics and cryptic species

    International Nuclear Information System (INIS)

    McPheron, Bruce A.

    2000-01-01

    Does the definition of a species matter for pest management purposes? Taxonomists provide us with tools - usually morphological characters - to identify a group of organisms that we call a species. The implication of this identification is that all of the individuals that fit the provided description are members of the species in question. The taxonomists have considered the range of variation among individuals in defining the species, but this variation is often forgotten when we take the concept of species to the level of management. Just as there is morphological variation among individuals, there is also variation in practically any character we might imagine, which has implications for the short and long term success of our management tactics. The rich literature on insecticide resistance should be a constant reminder of the fact that the pressure on pest survival and reproduction applied by our management approaches frequently leads to evolutionary changes within the pest species. The degree of variation within a particular species is a defining characteristic of that species. This level of variability may have very important implications for successful management, so it is very important to measure variation and, whenever possible, the genetic basis of that variation, in a target species. Population genetic approaches can provide evidence of genetic structure (or lack thereof) among populations of a species. These types of data can be used to discuss the movement of pest populations on a local or global scale. In other cases, we may have a complex of species that share some, but not all, characteristics. Species complexes that share morphological characters (i.e., cannot be easily distinguished) but not biological characters are referred to as sibling or cryptic species

  2. A mathematical model of a crocodilian population using delay-differential equations.

    Science.gov (United States)

    Gallegos, Angela; Plummer, Tenecia; Uminsky, David; Vega, Cinthia; Wickman, Clare; Zawoiski, Michael

    2008-11-01

    The crocodilia have multiple interesting characteristics that affect their population dynamics. They are among several reptile species which exhibit temperature-dependent sex determination (TSD) in which the temperature of egg incubation determines the sex of the hatchlings. Their life parameters, specifically birth and death rates, exhibit strong age-dependence. We develop delay-differential equation (DDE) models describing the evolution of a crocodilian population. In using the delay formulation, we are able to account for both the TSD and the age-dependence of the life parameters while maintaining some analytical tractability. In our single-delay model we also find an equilibrium point and prove its local asymptotic stability. We numerically solve the different models and investigate the effects of multiple delays on the age structure of the population as well as the sex ratio of the population. For all models we obtain very strong agreement with the age structure of crocodilian population data as reported in Smith and Webb (Aust. Wild. Res. 12, 541-554, 1985). We also obtain reasonable values for the sex ratio of the simulated population.

  3. The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

    Science.gov (United States)

    Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

    2015-04-01

    Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

  4. Environmental variability uncovers disruptive effects of species' interactions on population dynamics.

    Science.gov (United States)

    Gudmundson, Sara; Eklöf, Anna; Wennergren, Uno

    2015-08-07

    How species respond to changes in environmental variability has been shown for single species, but the question remains whether these results are transferable to species when incorporated in ecological communities. Here, we address this issue by analysing the same species exposed to a range of environmental variabilities when (i) isolated or (ii) embedded in a food web. We find that all species in food webs exposed to temporally uncorrelated environments (white noise) show the same type of dynamics as isolated species, whereas species in food webs exposed to positively autocorrelated environments (red noise) can respond completely differently compared with isolated species. This is owing to species following their equilibrium densities in a positively autocorrelated environment that in turn enables species-species interactions to come into play. Our results give new insights into species' response to environmental variation. They especially highlight the importance of considering both species' interactions and environmental autocorrelation when studying population dynamics in a fluctuating environment. © 2015 The Author(s).

  5. on the apllication of single specie dynamic population model 306

    African Journals Online (AJOL)

    pc

    Bayero Journal of Pure and Applied Sciences, 10(1): 306 - 311. Received: ... The Method of mathematical models of Malthus and Verhults were applied on ten years data collected from ..... and Time, Cambridge University Press,. (1991), 6 – 9.

  6. Central-marginal population dynamics in species invasions

    Directory of Open Access Journals (Sweden)

    Qinfeng eGuo

    2014-06-01

    Full Text Available The species’ range limits and associated central-marginal (C-M; i.e., from species range center to margin population dynamics continue to draw increasing attention because of their importance for current emerging issues such as biotic invasions and epidemic diseases under global change. Previous studies have mainly focused on species borders and C-M process in natural settings for native species. More recently, growing efforts are devoted to examine the C-M patterns and process for invasive species partly due to their relatively short history, highly dynamic populations, and management implications. Here I examine recent findings and information gaps related to (1 the C-M population dynamics linked to species invasions, and (2 the possible effects of climate change and land use on the C-M patterns and processes. Unlike most native species that are relatively stable (some even having contracting populations or ranges, many invasive species are still spreading fast and form new distribution or abundance centers. Because of the strong nonlinearity of population demographic or vital rates (i.e. birth, death, immigration and emigration across the C-M gradients and the increased complexity of species ranges due to habitat fragmentation, multiple introductions, range-wide C-M comparisons and simulation involving multiple vital rates are needed in the future.

  7. Combining a weed traits database with a population dynamics model predicts shifts in weed communities.

    Science.gov (United States)

    Storkey, J; Holst, N; Bøjer, O Q; Bigongiali, F; Bocci, G; Colbach, N; Dorner, Z; Riemens, M M; Sartorato, I; Sønderskov, M; Verschwele, A

    2015-04-01

    A functional approach to predicting shifts in weed floras in response to management or environmental change requires the combination of data on weed traits with analytical frameworks that capture the filtering effect of selection pressures on traits. A weed traits database (WTDB) was designed, populated and analysed, initially using data for 19 common European weeds, to begin to consolidate trait data in a single repository. The initial choice of traits was driven by the requirements of empirical models of weed population dynamics to identify correlations between traits and model parameters. These relationships were used to build a generic model, operating at the level of functional traits, to simulate the impact of increasing herbicide and fertiliser use on virtual weeds along gradients of seed weight and maximum height. The model generated 'fitness contours' (defined as population growth rates) within this trait space in different scenarios, onto which two sets of weed species, defined as common or declining in the UK, were mapped. The effect of increasing inputs on the weed flora was successfully simulated; 77% of common species were predicted to have stable or increasing populations under high fertiliser and herbicide use, in contrast with only 29% of the species that have declined. Future development of the WTDB will aim to increase the number of species covered, incorporate a wider range of traits and analyse intraspecific variability under contrasting management and environments.

  8. Occupancy modeling and estimation of the holiday darter species complex within the Etowah River system

    Science.gov (United States)

    Anderson, Gregory B.; Freeman, Mary C.; Hagler, Megan M.; Freeman, Byron J.

    2012-01-01

    Documenting the status of rare fishes is a crucial step in effectively managing populations and implementing regulatory mechanisms of protection. In recent years, site occupancy has become an increasingly popular metric for assessing populations, but species distribution models that do not account for imperfect detection can underestimate the proportion of sites occupied and the strength of the relationship with a hypothesized covariate. However, valid detection requires temporal or spatial replication, which is often not feasible due to logistical or budget constraints. In this study, we used a method that allowed for spatial replication during a single visit to evaluate the current status of the holiday darter species complex, Etheostoma sp. cf. E. brevirostrum, within the Etowah River system. Moreover, the modeling approach used in this study facilitated comparisons of factors influencing stream occupancy as well as species detection within sites. The results suggest that there is less habitat available for the Etowah holiday darter form (Etheostoma sp. cf. E. brevirostrum B) than for the Amicalola holiday darter form (Etheostoma sp. cf. E. brevirostrum A). Additionally, occupancy models suggest that even small decreases in forest cover within these headwater systems adversely affect holiday darter populations.

  9. Solvable single-species aggregation-annihilation model for chain-shaped cluster growth

    International Nuclear Information System (INIS)

    Ke Jianhong; Lin Zhenquan; Zheng Yizhuang; Chen Xiaoshuang; Lu Wei

    2007-01-01

    We propose a single-species aggregation-annihilation model, in which an aggregation reaction between two clusters produces an active cluster and an annihilation reaction produces an inert one. By means of the mean-field rate equation, we respectively investigate the kinetic scaling behaviours of three distinct systems. The results exhibit that: (i) for the general aggregation-annihilation system, the size distribution of active clusters consistently approaches the conventional scaling form; (ii) for the system with the self-degeneration of the cluster's activities, it takes the modified scaling form; and (iii) for the system with the self-closing of active clusters, it does not scale. Moreover, the size distribution of inert clusters with small size takes a power-law form, while that of large inert clusters obeys the scaling law. The results also show that all active clusters will eventually transform into inert ones and the inert clusters of any size can be produced by such an aggregation-annihilation process. This model can be used to mimic the chain-shaped cluster growth and can provide some useful predictions for the kinetic behaviour of the system

  10. Combining demographic and genetic factors to assess population vulnerability in stream species

    Science.gov (United States)

    Erin L, Landguth; Muhlfeld, Clint C.; Jones, Leslie W.; Waples, Robin S.; Whited, Diane; Lowe, Winsor H.; Lucotch, John; Neville, Helen; Luikart, Gordon

    2014-01-01

    Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially explicit, individual-based, demographic and genetic (demogenetic) assessments with environmental variables. To show its potential utility, we simulated a hypothetical network of 19 migratory riverine populations (e.g., salmonids) using a riverscape connectivity and demogenetic model (CDFISH). We assessed how stream resistance to movement (a function of water temperature, fluvial distance, and physical barriers) might influence demogenetic connectivity, and hence, population vulnerability. We present demographic metrics (abundance, immigration, and change in abundance) and genetic metrics (diversity, differentiation, and change in differentiation), and combine them into a single vulnerability index for identifying populations at risk of extirpation. We considered four realistic scenarios that illustrate the relative sensitivity of these metrics for early detection of reduced connectivity: (1) maximum resistance due to high water temperatures throughout the network, (2) minimum resistance due to low water temperatures throughout the network, (3) increased resistance at a tributary junction caused by a partial barrier, and (4) complete isolation of a tributary, leaving resident individuals only. We then applied this demogenetic framework using empirical data for a bull trout (Salvelinus confluentus) metapopulation in the upper Flathead River system, Canada and USA, to assess how current and predicted future stream warming may influence population vulnerability. Results suggest that warmer water temperatures and associated barriers to movement (e.g., low flows, dewatering) are predicted to fragment suitable habitat for migratory salmonids, resulting in the loss

  11. Studying Validity of Single-Fluid Model in Inertial Confinement Fusion

    International Nuclear Information System (INIS)

    Gu Jian-Fa; Fan Zheng-Feng; Dai Zhen-Sheng; Ye Wen-Hua; Pei Wen-Bing; Zhu Shao-Ping

    2014-01-01

    The validity of single-fluid model in inertial confinement fusion simulations is studied by comparing the results of the multi- and single-fluid models. The multi-fluid model includes the effects of collision and interpenetration between fluid species. By simulating the collision of fluid species, steady-state shock propagation into the thin DT gas and expansion of hohlraum Au wall heated by lasers, the results show that the validity of single-fluid model is strongly dependent on the ratio of the characteristic length of the simulated system to the particle mean free path. When the characteristic length L is one order larger than the mean free path λ, the single-fluid model's results are found to be in good agreement with the multi-fluid model's simulations, and the modeling of single-fluid remains valid. If the value of L/λ is lower than 10, the interpenetration between fluid species is significant, and the single-fluid simulations show some unphysical results; while the multi-fluid model can describe well the interpenetration and mix phenomena, and give more reasonable results. (physics of gases, plasmas, and electric discharges)

  12. Modelling population dynamics model formulation, fitting and assessment using state-space methods

    CERN Document Server

    Newman, K B; Morgan, B J T; King, R; Borchers, D L; Cole, D J; Besbeas, P; Gimenez, O; Thomas, L

    2014-01-01

    This book gives a unifying framework for estimating the abundance of open populations: populations subject to births, deaths and movement, given imperfect measurements or samples of the populations.  The focus is primarily on populations of vertebrates for which dynamics are typically modelled within the framework of an annual cycle, and for which stochastic variability in the demographic processes is usually modest. Discrete-time models are developed in which animals can be assigned to discrete states such as age class, gender, maturity,  population (within a metapopulation), or species (for multi-species models). The book goes well beyond estimation of abundance, allowing inference on underlying population processes such as birth or recruitment, survival and movement. This requires the formulation and fitting of population dynamics models.  The resulting fitted models yield both estimates of abundance and estimates of parameters characterizing the underlying processes.  

  13. Population Genetic Structure and Species Status of Asiatic Toads (Bufo gargarizans) in Western China.

    Science.gov (United States)

    Wen, Guannan; Yang, Weizhao; Fu, Jinzhong

    2015-10-01

    We investigated the population genetic structure of Asiatic toads (Bufo gargarizans) from the mountains of western China to determine their species status, using genotypic data of ten microsatellite DNA loci and DNA sequences from one mitochondrial gene. A total of 197 samples from eight sites were examined, which cover a large range of elevations (559-3457 m), as well as all three traditionally defined species (or subspecies). AMOVA did not reveal any particularly large among-groups structure, whether the sites were grouped by drainage, elevation, region, or species (subspecies). Individual assignment tests placed all samples into two genetic clusters, which largely corresponded to their geographic locations. An isolation-by-distance pattern was also detected when an outlier population (site 3) was excluded. Furthermore, a mitochondrial gene tree revealed deep divergence among haplotypes, sometimes within the same site. The clade patterns were partially associated with geographic distribution but had no resemblance to the traditional 2- or 3-species classification. Overall, these toad populations harbor a large amount of genetic diversity and have very high population differentiation, but taken together the evidence suggests that all populations belong to a single species. Our results are consistent with most previous molecular studies, and we recommend using Bufo gargarizans to represent all Asiatic toad populations from western China without subspecies division.

  14. Fire management strategies to maintain species population processes in a fragmented landscape of fire-interval extremes.

    Science.gov (United States)

    Tulloch, Ayesha I T; Pichancourt, Jean-Baptiste; Gosper, Carl R; Sanders, Angela; Chadès, Iadine

    2016-10-01

    Changed fire regimes have led to declines of fire-regime-adapted species and loss of biodiversity globally. Fire affects population processes of growth, reproduction, and dispersal in different ways, but there is little guidance about the best fire regime(s) to maintain species population processes in fire-prone ecosystems. We use a process-based approach to determine the best range of fire intervals for keystone plant species in a highly modified Mediterranean ecosystem in southwestern Australia where current fire regimes vary. In highly fragmented areas, fires are few due to limited ignitions and active suppression of wildfire on private land, while in highly connected protected areas fires are frequent and extensive. Using matrix population models, we predict population growth of seven Banksia species under different environmental conditions and patch connectivity, and evaluate the sensitivity of species survival to different fire management strategies and burning intervals. We discover that contrasting, complementary patterns of species life-histories with time since fire result in no single best fire regime. All strategies result in the local patch extinction of at least one species. A small number of burning strategies secure complementary species sets depending on connectivity and post-fire growing conditions. A strategy of no fire always leads to fewer species persisting than prescribed fire or random wildfire, while too-frequent or too-rare burning regimes lead to the possible local extinction of all species. In low landscape connectivity, we find a smaller range of suitable fire intervals, and strategies of prescribed or random burning result in a lower number of species with positive growth rates after 100 years on average compared with burning high connectivity patches. Prescribed fire may reduce or increase extinction risk when applied in combination with wildfire depending on patch connectivity. Poor growing conditions result in a significantly

  15. Using species distribution model to estimate the wintering population size of the endangered scaly-sided merganser in China.

    Directory of Open Access Journals (Sweden)

    Qing Zeng

    Full Text Available Scaly-sided Merganser is a globally endangered species restricted to eastern Asia. Estimating its population is difficult and considerable gap exists between populations at its breeding grounds and wintering sites. In this study, we built a species distribution model (SDM using Maxent with presence-only data to predict the potential wintering habitat for Scaly-sided Merganser in China. Area under the receiver operating characteristic curve (AUC method suggests high predictive power of the model (training and testing AUC were 0.97 and 0.96 respectively. The most significant environmental variables included annual mean temperature, mean temperature of coldest quarter, minimum temperature of coldest month and precipitation of driest quarter. Suitable conditions for Scaly-sided Merganser are predicted in the middle and lower reaches of the Yangtze River, especially in Jiangxi, Hunan and Hubei Provinces. The predicted suitable habitat embraces 6,984 km of river. Based on survey results from three consecutive winters (2010-2012 and previous studies, we estimated that the entire wintering population of Scaly-sided Merganser in China to be 3,561 ± 478 individuals, which is consistent with estimate in its breeding ground.

  16. An inbreeding model of associative overdominance during a population bottleneck.

    Science.gov (United States)

    Bierne, N; Tsitrone, A; David, P

    2000-08-01

    Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect.

  17. Linking an ecosystem model and a landscape model to study forest species response to climate warming

    Science.gov (United States)

    Hong S. He; David J. Mladenoff; Thomas R. Crow

    1999-01-01

    No single model can address forest change from single tree to regional scales. We discuss a framework linking an ecosystem process model {LINKAGES) with a spatial landscape model (LANDIS) to examine forest species responses to climate warming for a large, heterogeneous landscape in northern Wisconsin, USA. Individual species response at the ecosystem scale was...

  18. Actual and potential use of population viability analyses in recovery of plant species listed under the US endangered species act.

    Science.gov (United States)

    Zeigler, Sara L; Che-Castaldo, Judy P; Neel, Maile C

    2013-12-01

    Use of population viability analyses (PVAs) in endangered species recovery planning has been met with both support and criticism. Previous reviews promote use of PVA for setting scientifically based, measurable, and objective recovery criteria and recommend improvements to increase the framework's utility. However, others have questioned the value of PVA models for setting recovery criteria and assert that PVAs are more appropriate for understanding relative trade-offs between alternative management actions. We reviewed 258 final recovery plans for 642 plants listed under the U.S. Endangered Species Act to determine the number of plans that used or recommended PVA in recovery planning. We also reviewed 223 publications that describe plant PVAs to assess how these models were designed and whether those designs reflected previous recommendations for improvement of PVAs. Twenty-four percent of listed species had recovery plans that used or recommended PVA. In publications, the typical model was a matrix population model parameterized with ≤5 years of demographic data that did not consider stochasticity, genetics, density dependence, seed banks, vegetative reproduction, dormancy, threats, or management strategies. Population growth rates for different populations of the same species or for the same population at different points in time were often statistically different or varied by >10%. Therefore, PVAs parameterized with underlying vital rates that vary to this degree may not accurately predict recovery objectives across a species' entire distribution or over longer time scales. We assert that PVA, although an important tool as part of an adaptive-management program, can help to determine quantitative recovery criteria only if more long-term data sets that capture spatiotemporal variability in vital rates become available. Lacking this, there is a strong need for viable and comprehensive methods for determining quantitative, science-based recovery criteria for

  19. Phenotypic plasticity and population differentiation in an ongoing species invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available The ability to succeed in diverse conditions is a key factor allowing introduced species to successfully invade and spread across new areas. Two non-exclusive factors have been suggested to promote this ability: adaptive phenotypic plasticity of individuals, and the evolution of locally adapted populations in the new range. We investigated these individual and population-level factors in Polygonum cespitosum, an Asian annual that has recently become invasive in northeastern North America. We characterized individual fitness, life-history, and functional plasticity in response to two contrasting glasshouse habitat treatments (full sun/dry soil and understory shade/moist soil in 165 genotypes sampled from nine geographically separate populations representing the range of light and soil moisture conditions the species inhabits in this region. Polygonum cespitosum genotypes from these introduced-range populations expressed broadly similar plasticity patterns. In response to full sun, dry conditions, genotypes from all populations increased photosynthetic rate, water use efficiency, and allocation to root tissues, dramatically increasing reproductive fitness compared to phenotypes expressed in simulated understory shade. Although there were subtle among-population differences in mean trait values as well as in the slope of plastic responses, these population differences did not reflect local adaptation to environmental conditions measured at the population sites of origin. Instead, certain populations expressed higher fitness in both glasshouse habitat treatments. We also compared the introduced-range populations to a single population from the native Asian range, and found that the native population had delayed phenology, limited functional plasticity, and lower fitness in both experimental environments compared with the introduced-range populations. Our results indicate that the future spread of P. cespitosum in its introduced range will likely be

  20. POPULATION STRUCTURES OF FOUR TREE SPECIES IN LOGGED-OVER TROPICAL FOREST IN SOUTH PAPUA, INDONESIA: AN INTEGRAL PROJECTION MODEL APPROACH

    Directory of Open Access Journals (Sweden)

    Relawan kuswandi

    2015-12-01

    Full Text Available Selective logging has been taking place in Papua for several decades. In contrast, very little is known about the stand structure in post-logged forest. Hence, this paper investigates stand structures in logged-over area of tropical forest in South Papua. Four species were selected in three one-hectare permanent sample plots (PSPs: Vatica rassak, Syzygium sp, Litsea timoriana and Canarium asperum. PSPs were located in the forest concession area of PT. Tunas Sawaerma in Assiki, Boven Digul, in South Papua. Data sets comprised measurements made in 2005 and 2012 consisting of species, diameter at breast height (DBH, mortality and number of tree of each species. Integral Projection Models (IPMs were developed, taking into account mortality, growth, recruitment and fecundity. Results show the pattern of stand structures of the four species were more or less similar, i.e. more individual trees were present in the small diameter classes than in the larger diameter classes. The general pattern of the individual distribution of the four species is the typical reverse-J shape. Syzygium sp. has a greater number of individuals in the small diameter classes than the other three species. Population growth rates (λ are above one, indicating that the stand structures of the population dynamics of the four species are recuperating. Conclusively, these results suggest that species composition and population structure in these logged-over forests are recovering increasingly.

  1. Modeling Population Growth and Extinction

    Science.gov (United States)

    Gordon, Sheldon P.

    2009-01-01

    The exponential growth model and the logistic model typically introduced in the mathematics curriculum presume that a population grows exclusively. In reality, species can also die out and more sophisticated models that take the possibility of extinction into account are needed. In this article, two extensions of the logistic model are considered,…

  2. Fish population studies using parasites from the Southeastern Pacific Ocean: considering host population changes and species body size as sources of variability of parasite communities.

    Science.gov (United States)

    George-Nascimento, Mario; Oliva, Marcelo

    2015-01-01

    Research using parasites in fish population studies in the South Eastern Pacific (SEP) is summarized. There are 27 such studies (snapshots mainly) in single host species sampled at different geographic localities and at somewhat similar times. They have been devoted mainly to economically important species, though others on coastal and intertidal fish or on less- or non-commercial species provide insights on scales of temporal and spatial variation of parasite infracommunities. Later, we assess whether the probability of harbouring parasites depends on the host species body size. Our results indicate that a stronger tool for fish population studies may be developed under regular (long term) scrutiny of parasite communities, especially of small fish host species, due to their larger variability in richness, abundance and total biomass, than in large fish species. Finally, it might also be necessary to consider the effects of fishing on parasite communities as well as the natural oscillations (coupled or not) of host and parasite populations.

  3. Factors affecting GEBV accuracy with single-step Bayesian models.

    Science.gov (United States)

    Zhou, Lei; Mrode, Raphael; Zhang, Shengli; Zhang, Qin; Li, Bugao; Liu, Jian-Feng

    2018-01-01

    A single-step approach to obtain genomic prediction was first proposed in 2009. Many studies have investigated the components of GEBV accuracy in genomic selection. However, it is still unclear how the population structure and the relationships between training and validation populations influence GEBV accuracy in terms of single-step analysis. Here, we explored the components of GEBV accuracy in single-step Bayesian analysis with a simulation study. Three scenarios with various numbers of QTL (5, 50, and 500) were simulated. Three models were implemented to analyze the simulated data: single-step genomic best linear unbiased prediction (GBLUP; SSGBLUP), single-step BayesA (SS-BayesA), and single-step BayesB (SS-BayesB). According to our results, GEBV accuracy was influenced by the relationships between the training and validation populations more significantly for ungenotyped animals than for genotyped animals. SS-BayesA/BayesB showed an obvious advantage over SSGBLUP with the scenarios of 5 and 50 QTL. SS-BayesB model obtained the lowest accuracy with the 500 QTL in the simulation. SS-BayesA model was the most efficient and robust considering all QTL scenarios. Generally, both the relationships between training and validation populations and LD between markers and QTL contributed to GEBV accuracy in the single-step analysis, and the advantages of single-step Bayesian models were more apparent when the trait is controlled by fewer QTL.

  4. Determinants of bird conservation-action implementation and associated population trends of threatened species.

    Science.gov (United States)

    Luther, David A; Brooks, Thomas M; Butchart, Stuart H M; Hayward, Matt W; Kester, Marieke E; Lamoreux, John; Upgren, Amy

    2016-12-01

    Conservation actions, such as habitat protection, attempt to halt the loss of threatened species and help their populations recover. The efficiency and the effectiveness of actions have been examined individually. However, conservation actions generally occur simultaneously, so the full suite of implemented conservation actions should be assessed. We used the conservation actions underway for all threatened and near-threatened birds of the world (International Union for Conservation of Nature Red List of Threatened Species) to assess which biological (related to taxonomy and ecology) and anthropogenic (related to geoeconomics) factors were associated with the implementation of different classes of conservation actions. We also assessed which conservation actions were associated with population increases in the species targeted. Extinction-risk category was the strongest single predictor of the type of conservation actions implemented, followed by landmass type (continent, oceanic island, etc.) and generation length. Species targeted by invasive nonnative species control or eradication programs, ex situ conservation, international legislation, reintroduction, or education, and awareness-raising activities were more likely to have increasing populations. These results illustrate the importance of developing a predictive science of conservation actions and the relative benefits of each class of implemented conservation action for threatened and near-threatened birds worldwide. © 2016 Society for Conservation Biology.

  5. Mechanistic species distribution modeling reveals a niche shift during invasion.

    Science.gov (United States)

    Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M

    2017-06-01

    Niche shifts of nonnative plants can occur when they colonize novel climatic conditions. However, the mechanistic basis for niche shifts during invasion is poorly understood and has rarely been captured within species distribution models. We quantified the consequence of between-population variation in phenology for invasion of common ragweed (Ambrosia artemisiifolia L.) across Europe. Ragweed is of serious concern because of its harmful effects as a crop weed and because of its impact on public health as a major aeroallergen. We developed a forward mechanistic species distribution model based on responses of ragweed development rates to temperature and photoperiod. The model was parameterized and validated from the literature and by reanalyzing data from a reciprocal common garden experiment in which native and invasive populations were grown within and beyond the current invaded range. It could therefore accommodate between-population variation in the physiological requirements for flowering, and predict the potentially invaded ranges of individual populations. Northern-origin populations that were established outside the generally accepted climate envelope of the species had lower thermal requirements for bud development, suggesting local adaptation of phenology had occurred during the invasion. The model predicts that this will extend the potentially invaded range northward and increase the average suitability across Europe by 90% in the current climate and 20% in the future climate. Therefore, trait variation observed at the population scale can trigger a climatic niche shift at the biogeographic scale. For ragweed, earlier flowering phenology in established northern populations could allow the species to spread beyond its current invasive range, substantially increasing its risk to agriculture and public health. Mechanistic species distribution models offer the possibility to represent niche shifts by varying the traits and niche responses of individual

  6. PDEAR model prediction of Protea species in years 2070-2100

    Science.gov (United States)

    Guo, Danni; Guo, Renkuan; Midgley, Guy F.; Rebelo, A. G.

    2009-10-01

    Global warming and climate changes are changing the environment and therefore changing the distribution and behaviour of the plant species. Plant species often move and change their distributions as they find their original habitats are no longer suitable to their needs. It is therefore important to establish a statistical model to catch up the movement and patterns of the endangered species in order to effectively manage environmental protection under the inevitable biodiversity changes that are taking place. In this paper, we are focusing on the population category of rare Proteas that has an estimated population size from 1 to 10 per sample site, which is very small. We used the partial differential equation associated regression (PDEAR) model, which merges the partial differential equation theory, (statistical) linear model theory and random fuzzy variable theory together into a efficient small-sample oriented model, for the spatial pattern changing analysis. The regression component in a PDEAR model is in nature a special random fuzzy multivariate regression model. We developed a bivariate model for investigating the impacts from rainfall and temperature on the Protea species in average sense in the population size of 1 to 10, in the Cape Floristic Region, from 1992 to 2002, South Africa. Under same the average biodiversity structure assumptions, we explore the future spatial change patterns of Protea species in the population size of 1 to 10 with future (average) predicted rainfall and temperature. The spatial distribution and patterns are clearly will help us to explore global climate changing impacts on endangered species.

  7. Defense of single-factor models of population regulation

    International Nuclear Information System (INIS)

    Tamarin, R.H.

    1978-01-01

    I reject a multifactorial approach to the study of the regulation of animal populations for two reasons. First, a mechanism suggested by Chitty, that has natural selection at its base, has not been adequately tested. Second, the multifactorial model suggested by Lidicker is untestable because of its vagueness. As a middle ground, I suggest a model that has natural selection as its mechanism, but is multifacturial because it allows many parameters to be the selective agents. I particularly emphasize prediction and selective dispersal. Methods to test this model are suggested

  8. Establishing endangered species recovery criteria using predictive simulation modeling

    Science.gov (United States)

    McGowan, Conor P.; Catlin, Daniel H.; Shaffer, Terry L.; Gratto-Trevor, Cheri L.; Aron, Carol

    2014-01-01

    Listing a species under the Endangered Species Act (ESA) and developing a recovery plan requires U.S. Fish and Wildlife Service to establish specific and measurable criteria for delisting. Generally, species are listed because they face (or are perceived to face) elevated risk of extinction due to issues such as habitat loss, invasive species, or other factors. Recovery plans identify recovery criteria that reduce extinction risk to an acceptable level. It logically follows that the recovery criteria, the defined conditions for removing a species from ESA protections, need to be closely related to extinction risk. Extinction probability is a population parameter estimated with a model that uses current demographic information to project the population into the future over a number of replicates, calculating the proportion of replicated populations that go extinct. We simulated extinction probabilities of piping plovers in the Great Plains and estimated the relationship between extinction probability and various demographic parameters. We tested the fit of regression models linking initial abundance, productivity, or population growth rate to extinction risk, and then, using the regression parameter estimates, determined the conditions required to reduce extinction probability to some pre-defined acceptable threshold. Binomial regression models with mean population growth rate and the natural log of initial abundance were the best predictors of extinction probability 50 years into the future. For example, based on our regression models, an initial abundance of approximately 2400 females with an expected mean population growth rate of 1.0 will limit extinction risk for piping plovers in the Great Plains to less than 0.048. Our method provides a straightforward way of developing specific and measurable recovery criteria linked directly to the core issue of extinction risk. Published by Elsevier Ltd.

  9. A trans-national monarch butterfly population model and implications for regional conservation priorities

    Science.gov (United States)

    Oberhauser, Karen; Wiederholt, Ruscena; Diffendorfer, James E.; Semmens, Darius J.; Ries, Leslie; Thogmartin, Wayne E.; Lopez-Hoffman, Laura; Semmens, Brice

    2017-01-01

    1. The monarch has undergone considerable population declines over the past decade, and the governments of Mexico, Canada, and the United States have agreed to work together to conserve the species.2. Given limited resources, understanding where to focus conservation action is key for widespread species like monarchs. To support planning for continental-scale monarch habitat restoration, we address the question of where restoration efforts are likely to have the largest impacts on monarch butterfly (Danaus plexippus Linn.) population growth rates.3. We present a spatially explicit demographic model simulating the multi-generational annual cycle of the eastern monarch population, and use the model to examine management scenarios, some of which focus on particular regions of North America.4. Improving the monarch habitat in the north central or southern parts of the monarch range yields a slightly greater increase in the population growth rate than restoration in other regions. However, combining restoration efforts across multiple regions yields population growth rates above 1 with smaller simulated improvements in habitat per region than single-region strategies.5. Synthesis and applications: These findings suggest that conservation investment in projects across the full monarch range will be more effective than focusing on one or a few regions, and will require international cooperation across many land use categories.

  10. Population modelling to compare chronic external radiotoxicity between individual and population endpoints in four taxonomic groups

    International Nuclear Information System (INIS)

    Alonzo, Frédéric; Hertel-Aas, Turid; Real, Almudena; Lance, Emilie; Garcia-Sanchez, Laurent; Bradshaw, Clare; Vives i Batlle, Jordi; Oughton, Deborah H.; Garnier-Laplace, Jacqueline

    2016-01-01

    In this study, we modelled population responses to chronic external gamma radiation in 12 laboratory species (including aquatic and soil invertebrates, fish and terrestrial mammals). Our aim was to compare radiosensitivity between individual and population endpoints and to examine how internationally proposed benchmarks for environmental radioprotection protected species against various risks at the population level. To do so, we used population matrix models, combining life history and chronic radiotoxicity data (derived from laboratory experiments and described in the literature and the FREDERICA database) to simulate changes in population endpoints (net reproductive rate R_0, asymptotic population growth rate λ, equilibrium population size N_e_q) for a range of dose rates. Elasticity analyses of models showed that population responses differed depending on the affected individual endpoint (juvenile or adult survival, delay in maturity or reduction in fecundity), the considered population endpoint (R_0, λ or N_e_q) and the life history of the studied species. Among population endpoints, net reproductive rate R_0 showed the lowest EDR_1_0 (effective dose rate inducing 10% effect) in all species, with values ranging from 26 μGy h"−"1 in the mouse Mus musculus to 38,000 μGy h"−"1 in the fish Oryzias latipes. For several species, EDR_1_0 for population endpoints were lower than the lowest EDR_1_0 for individual endpoints. Various population level risks, differing in severity for the population, were investigated. Population extinction (predicted when radiation effects caused population growth rate λ to decrease below 1, indicating that no population growth in the long term) was predicted for dose rates ranging from 2700 μGy h"−"1 in fish to 12,000 μGy h"−"1 in soil invertebrates. A milder risk, that population growth rate λ will be reduced by 10% of the reduction causing extinction, was predicted for dose rates ranging from 24 μGy h"−"1

  11. Comparative toxicity of a brominated flame retardant (tetrabromobisphenol A) on microalgae with single and multi-species bioassays.

    Science.gov (United States)

    Debenest, Timothée; Petit, Anne-Nöelle; Gagné, François; Kohli, Mohan; Nguyen, Nien; Blaise, Christian

    2011-09-01

    The potential threat of emerging chemicals to the aquatic flora is a major issue. The purpose of the study was to develop a multispecies microalgae test in order to determine the impact of species interactions on the cytoxicity of an emergent toxic contaminant: the tetrabromobisphenol A (TBBPA). Single and multi-species tests were thus performed to study the effects of this flame retardant on two microalgae (Pseudokirchneriella subcapitata and Nitzschia palea) commonly observed in freshwater. A synthetic medium was designed to allow the growth of both species. The algae were exposed to 1.8, 4.8, 9.2, 12.9 and 16.5 μM of TBBPA for 72 h. After staining with fluorescein diacetate (FDA), viable cells of each alga species were analyzed by flow cytometry based on chlorophyll autofluorescence and intracellular esterase activity. Density and abundance of viable cells were assessed to follow the population growth and the cell viability. In TBBPA treated samples, the growth of the two microalgae was significantly inhibited at the three highest concentrations (9.2, 12.9 and 16.5 μM) in the two tests. At the end of the experiment (t=72 h), the cell viability was also significantly smaller at these concentrations. The decreases of growth rate and viable cell abundance in TBBPA treated populations of N. palea were significantly higher in multi-species test in comparison with the single-species test. No significant differences were noticed between the two tests for P. subcapitata populations exposed to TBBPA. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

  12. Mapping of the stochastic Lotka-Volterra model to models of population genetics and game theory

    Science.gov (United States)

    Constable, George W. A.; McKane, Alan J.

    2017-08-01

    The relationship between the M -species stochastic Lotka-Volterra competition (SLVC) model and the M -allele Moran model of population genetics is explored via timescale separation arguments. When selection for species is weak and the population size is large but finite, precise conditions are determined for the stochastic dynamics of the SLVC model to be mappable to the neutral Moran model, the Moran model with frequency-independent selection, and the Moran model with frequency-dependent selection (equivalently a game-theoretic formulation of the Moran model). We demonstrate how these mappings can be used to calculate extinction probabilities and the times until a species' extinction in the SLVC model.

  13. A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling.

    Science.gov (United States)

    Dalmaris, Eleftheria; Ramalho, Cristina E; Poot, Pieter; Veneklaas, Erik J; Byrne, Margaret

    2015-11-01

    A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia. Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM). A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction. Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had

  14. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  15. Morphological and genetic evolution in eastern populations of the Macrhybopsis aestivalis complex (Cypriniformes: Cyprinidae), with the descriptions of four new species.

    Science.gov (United States)

    Gilbert, Carter R; Mayden, Richard L; Powers, Steven L

    2017-03-30

    For many years the North American cyprinid fish Macrhybopsis aestivalis (common name: Speckled Chub) was regarded as a single widespread and morphologically variable species, occurring in rivers throughout much of the Mississippi Valley and geographically adjacent eastern Gulf slope drainages, west to the Rio Grande basin in Texas, New Mexico, and Mexico. Eisenhour (1997) completed a morphological study of western populations of the Speckled Chub, the results of which appeared thereafter in published form (Eisenhour 1999, 2004). He demonstrated the existence of five valid species west of the Mississippi River (aestivalis, marconis, australis, tetranema, hyostoma), of which the name aestivalis was shown to be restricted to the population occurring in the Rio Grande and the geographically adjacent Rio San Fernando system, in northeastern Mexico. Eisenhour (2004) considered populations throughout the middle Mississippi Valley and its major tributaries to be a single morphologically variable species (hyostoma), and he also indicated that populations of Macrhybopsis from eastern Gulf slope drainages may represent a complex of species. Genetic confirmation of Eisenhour's conclusions regarding western species appeared in the publication by Underwood et al. (2003), who also showed that western populations of M. hyostoma, as presently recognized, are genetically much more complex than previously considered.     Meanwhile, the present authors were involved in a companion study of eastern populations of Macrhybopsis, for which a genetic summary of the eastern Gulf coast species was published by Mayden & Powers (2004). Based on their findings, four species were recognized from southeastern drainages (identified as species A-D), although no formal taxonomic descriptions were included. Their genetic data, in combination with meristic, morphometric and other morphological data presented herein, form the basis for a revised classification of eastern Macrhybopsis populations

  16. Application of high-resolution DNA melting for genotyping in lepidopteran non-model species: Ostrinia furnacalis (Crambidae.

    Directory of Open Access Journals (Sweden)

    FengBo Li

    Full Text Available Development of an ideal marker system facilitates a better understanding of the genetic diversity in lepidopteran non-model organisms, which have abundant species, but relatively limited genomic resources. Single nucleotide polymorphisms (SNPs discovered within single-copy genes have proved to be desired markers, but SNP genotyping by current techniques remain laborious and expensive. High resolution melting (HRM curve analysis represents a simple, rapid and inexpensive genotyping method that is primarily confined to clinical and diagnostic studies. In this study, we evaluated the potential of HRM analysis for SNP genotyping in the lepidopteran non-model species Ostrinia furnacalis (Crambidae. Small amplicon and unlabeled probe assays were developed for the SNPs, which were identified in 30 females of O. furnacalis from 3 different populations by our direct sequencing. Both assays were then applied to genotype 90 unknown female DNA by prior mixing with known wild-type DNA. The genotyping results were compared with those that were obtained using bi-directional sequencing analysis. Our results demonstrated the efficiency and reliability of the HRM assays. HRM has the potential to provide simple, cost-effective genotyping assays and facilitates genotyping studies in any non-model lepidopteran species of interest.

  17. Process-based modeling of species' responses to climate change - a proof of concept using western North American trees

    Science.gov (United States)

    Evans, M. E.; Merow, C.; Record, S.; Menlove, J.; Gray, A.; Cundiff, J.; McMahon, S.; Enquist, B. J.

    2013-12-01

    Current attempts to forecast how species' distributions will change in response to climate change suffer under a fundamental trade-off: between modeling many species superficially vs. few species in detail (between correlative vs. mechanistic models). The goals of this talk are two-fold: first, we present a Bayesian multilevel modeling framework, dynamic range modeling (DRM), for building process-based forecasts of many species' distributions at a time, designed to address the trade-off between detail and number of distribution forecasts. In contrast to 'species distribution modeling' or 'niche modeling', which uses only species' occurrence data and environmental data, DRMs draw upon demographic data, abundance data, trait data, occurrence data, and GIS layers of climate in a single framework to account for two processes known to influence range dynamics - demography and dispersal. The vision is to use extensive databases on plant demography, distributions, and traits - in the Botanical Information and Ecology Network, the Forest Inventory and Analysis database (FIA), and the International Tree Ring Data Bank - to develop DRMs for North American trees. Second, we present preliminary results from building the core submodel of a DRM - an integral projection model (IPM) - for a sample of dominant tree species in western North America. IPMs are used to infer demographic niches - i.e., the set of environmental conditions under which population growth rate is positive - and project population dynamics through time. Based on >550,000 data points derived from FIA for nine tree species in western North America, we show IPM-based models of their current and future distributions, and discuss how IPMs can be used to forecast future forest productivity, mortality patterns, and inform efforts at assisted migration.

  18. Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

    Science.gov (United States)

    Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

    2018-01-01

    Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or

  19. Population modelling to compare chronic external radiotoxicity between individual and population endpoints in four taxonomic groups.

    Science.gov (United States)

    Alonzo, Frédéric; Hertel-Aas, Turid; Real, Almudena; Lance, Emilie; Garcia-Sanchez, Laurent; Bradshaw, Clare; Vives I Batlle, Jordi; Oughton, Deborah H; Garnier-Laplace, Jacqueline

    2016-02-01

    In this study, we modelled population responses to chronic external gamma radiation in 12 laboratory species (including aquatic and soil invertebrates, fish and terrestrial mammals). Our aim was to compare radiosensitivity between individual and population endpoints and to examine how internationally proposed benchmarks for environmental radioprotection protected species against various risks at the population level. To do so, we used population matrix models, combining life history and chronic radiotoxicity data (derived from laboratory experiments and described in the literature and the FREDERICA database) to simulate changes in population endpoints (net reproductive rate R0, asymptotic population growth rate λ, equilibrium population size Neq) for a range of dose rates. Elasticity analyses of models showed that population responses differed depending on the affected individual endpoint (juvenile or adult survival, delay in maturity or reduction in fecundity), the considered population endpoint (R0, λ or Neq) and the life history of the studied species. Among population endpoints, net reproductive rate R0 showed the lowest EDR10 (effective dose rate inducing 10% effect) in all species, with values ranging from 26 μGy h(-1) in the mouse Mus musculus to 38,000 μGy h(-1) in the fish Oryzias latipes. For several species, EDR10 for population endpoints were lower than the lowest EDR10 for individual endpoints. Various population level risks, differing in severity for the population, were investigated. Population extinction (predicted when radiation effects caused population growth rate λ to decrease below 1, indicating that no population growth in the long term) was predicted for dose rates ranging from 2700 μGy h(-1) in fish to 12,000 μGy h(-1) in soil invertebrates. A milder risk, that population growth rate λ will be reduced by 10% of the reduction causing extinction, was predicted for dose rates ranging from 24 μGy h(-1) in mammals to 1800 μGy h(-1) in

  20. Human population, grasshopper and plant species richness in European countries

    Science.gov (United States)

    Steck, Claude E.; Pautasso, Marco

    2008-11-01

    Surprisingly, several studies over large scales have reported a positive spatial correlation of people and biodiversity. This pattern has important implications for conservation and has been documented for well studied taxa such as plants, amphibians, reptiles, birds and mammals. However, it is unknown whether the pattern applies also to invertebrates other than butterflies and more work is needed to establish whether the species-people relationship is explained by both variables correlating with other environmental factors. We studied whether grasshopper species richness (Orthoptera, suborder Caelifera) is related to human population size in European countries. As expected, the number of Caelifera species increases significantly with increasing human population size. But this is not the case when controlling for country area, latitude and number of plant species. Variations in Caelifera species richness are primarily associated with variations in plant species richness. Caelifera species richness also increases with decreasing mean annual precipitation, Gross Domestic Product per capita (used as an indicator for economic development) and net fertility rate of the human population. Our analysis confirms the hypothesis that the broad-scale human population-biodiversity correlations can be explained by concurrent variations in factors other than human population size such as plant species richness, environmental productivity, or habitat heterogeneity. Nonetheless, more populated countries in Europe still have more Caelifera species than less populated countries and this poses a particular challenge for conservation.

  1. Statistical Models of Adaptive Immune populations

    Science.gov (United States)

    Sethna, Zachary; Callan, Curtis; Walczak, Aleksandra; Mora, Thierry

    The availability of large (104-106 sequences) datasets of B or T cell populations from a single individual allows reliable fitting of complex statistical models for naïve generation, somatic selection, and hypermutation. It is crucial to utilize a probabilistic/informational approach when modeling these populations. The inferred probability distributions allow for population characterization, calculation of probability distributions of various hidden variables (e.g. number of insertions), as well as statistical properties of the distribution itself (e.g. entropy). In particular, the differences between the T cell populations of embryonic and mature mice will be examined as a case study. Comparing these populations, as well as proposed mixed populations, provides a concrete exercise in model creation, comparison, choice, and validation.

  2. Population Genomics of Paramecium Species.

    Science.gov (United States)

    Johri, Parul; Krenek, Sascha; Marinov, Georgi K; Doak, Thomas G; Berendonk, Thomas U; Lynch, Michael

    2017-05-01

    Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance.

    Directory of Open Access Journals (Sweden)

    Gail S Robertson

    Full Text Available Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis. With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes

  4. A general modeling framework for describing spatially structured population dynamics

    Science.gov (United States)

    Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

    2017-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  5. Model-based analyses reveal insular population diversification and cryptic frog species in the Ischnocnema parva complex in the Atlantic forest of Brazil.

    Science.gov (United States)

    Gehara, Marcelo; Barth, Adriane; Oliveira, Eliana Faria de; Costa, Marco Antonio; Haddad, Célio Fernando Baptista; Vences, Miguel

    2017-07-01

    The Atlantic Forest (AF) of Brazil has long been recognized as a biodiversity conservation hotspot. Despite decades of studies the species inventory of this biome continues to increase with the discovery of cryptic diversity and the description of new species. Different diversification mechanisms have been proposed to explain the diversity in the region, including models of forest dynamics, barriers to gene flow and dispersal. Also, sea level change is thought to have influenced coastal diversification and isolated populations on continental islands. However, the timing and mode of diversification of insular populations in the AF region were rarely investigated. Here, we analyze the phylogeography and species diversity of the small-sized direct-developing frog Ischnocnema parva. These frogs are independent from water bodies but dependent on forest cover and high humidity, and provide good models to understand forest dynamics and insular diversification. Our analysis was based on DNA sequences for one mitochondrial and four nuclear genes of 71 samples from 18 localities including two islands, São Sebastião, municipality of Ilhabela, and Mar Virado, municipality of Ubatuba, both in the state of São Paulo. We use molecular taxonomic methods to show that I. parva is composed of six independently evolving lineages, with the nominal I. parva likely endemic to the type locality. The time-calibrated species tree shows that these lineages have diverged in the Pliocene and Pleistocene, suggesting the persistence of micro-refuges of forest in the AF. For the two insular populations we used approximate Bayesian computation to test different diversification hypotheses. Our findings support isolation with migration for São Sebastião population, with ∼1Mya divergence time, and isolation without migration for Mar Virado population, with ∼13Kya divergence time, suggesting a combination of different processes for diversification on AF islands. Copyright © 2017. Published

  6. Delay-induced Turing-like waves for one-species reaction-diffusion model on a network

    Science.gov (United States)

    Petit, Julien; Carletti, Timoteo; Asllani, Malbor; Fanelli, Duccio

    2015-09-01

    A one-species time-delay reaction-diffusion system defined on a complex network is studied. Traveling waves are predicted to occur following a symmetry-breaking instability of a homogeneous stationary stable solution, subject to an external nonhomogeneous perturbation. These are generalized Turing-like waves that materialize in a single-species populations dynamics model, as the unexpected byproduct of the imposed delay in the diffusion part. Sufficient conditions for the onset of the instability are mathematically provided by performing a linear stability analysis adapted to time-delayed differential equations. The method here developed exploits the properties of the Lambert W-function. The prediction of the theory are confirmed by direct numerical simulation carried out for a modified version of the classical Fisher model, defined on a Watts-Strogatz network and with the inclusion of the delay.

  7. Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico.

    Directory of Open Access Journals (Sweden)

    Baptiste Faure

    Full Text Available Hydrocarbon seepage is widespread and patchy in the Gulf of Mexico, and six species of symbiont containing bathymodiolin mussels are found on active seeps over wide and overlapping depth and geographic ranges. We use mitochondrial genes to discriminate among the previously known and a newly discovered species and to assess the connectivity among populations of the same species in the northern Gulf of Mexico (GoM. Our results generally validate the morphologically based distribution of the three previously known GoM species of Bathymodiolus, although we found that approximately 10% of the morphologically based identifications were incorrect and this resulted in some inaccuracies with respect to their previously assigned depth and geographical distribution patterns. These data allowed us to confirm that sympatry of two species of Bathymodiolus within a single patch of mussels is common. A new species of bathymodiolin, Bathymodiolus sp. nov., closely related to B. heckerae was also discovered. The two species live at the same depths but have not been found in sympatry and both have small effective population sizes. We found evidence for genetic structure within populations of the three species of Bathymodiolinae for which we had samples from multiple sites and suggest limited connectivity for populations at some sites. Despite relatively small sample sizes, genetic diversity indices suggest the largest population sizes for B. childressi and Tamu fisheri and the smallest for B. heckerae and B. sp. nov. among the GoM bathymodiolins. Moreover, we detected an excess of rare variants indicating recent demographic changes and population expansions for the four species of bathymodiolins from the Gulf of Mexico.

  8. A spatial ecosystem and populations dynamics model (SEAPODYM) Modeling of tuna and tuna-like populations

    Science.gov (United States)

    Lehodey, Patrick; Senina, Inna; Murtugudde, Raghu

    2008-09-01

    An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented to describe spatial dynamics of tuna and tuna-like species in the Pacific Ocean at monthly resolution over 1° grid-boxes. The simulations are driven by a bio-physical environment predicted from a coupled ocean physical-biogeochemical model. This new version of SEAPODYM includes expanded definitions of habitat indices, movements, and natural mortality based on empirical evidences. A thermal habitat of tuna species is derived from an individual heat budget model. The feeding habitat is computed according to the accessibility of tuna predator cohorts to different vertically migrating and non-migrating micronekton (mid-trophic) functional groups. The spawning habitat is based on temperature and the coincidence of spawning fish with presence or absence of predators and food for larvae. The successful larval recruitment is linked to spawning stock biomass. Larvae drift with currents, while immature and adult tuna can move of their own volition, in addition to being advected by currents. A food requirement index is computed to adjust locally the natural mortality of cohorts based on food demand and accessibility to available forage components. Together these mechanisms induce bottom-up and top-down effects, and intra- (i.e. between cohorts) and inter-species interactions. The model is now fully operational for running multi-species, multi-fisheries simulations, and the structure of the model allows a validation from multiple data sources. An application with two tuna species showing different biological characteristics, skipjack ( Katsuwonus pelamis) and bigeye ( Thunnus obesus), is presented to illustrate the capacity of the model to capture many important features of spatial dynamics of these two different tuna species in the Pacific Ocean. The actual validation is presented in a companion paper describing the approach to have a rigorous mathematical parameter optimization

  9. A probabilistic cellular automata model for the dynamics of a population driven by logistic growth and weak Allee effect

    Science.gov (United States)

    Mendonça, J. R. G.

    2018-04-01

    We propose and investigate a one-parameter probabilistic mixture of one-dimensional elementary cellular automata under the guise of a model for the dynamics of a single-species unstructured population with nonoverlapping generations in which individuals have smaller probability of reproducing and surviving in a crowded neighbourhood but also suffer from isolation and dispersal. Remarkably, the first-order mean field approximation to the dynamics of the model yields a cubic map containing terms representing both logistic and weak Allee effects. The model has a single absorbing state devoid of individuals, but depending on the reproduction and survival probabilities can achieve a stable population. We determine the critical probability separating these two phases and find that the phase transition between them is in the directed percolation universality class of critical behaviour.

  10. Population dynamics in changing environments: the case of an eruptive forest pest species.

    Science.gov (United States)

    Kausrud, Kyrre; Okland, Bjørn; Skarpaas, Olav; Grégoire, Jean-Claude; Erbilgin, Nadir; Stenseth, Nils Chr

    2012-02-01

    In recent decades we have seen rapid and co-occurring changes in landscape structure, species distributions and even climate as consequences of human activity. Such changes affect the dynamics of the interaction between major forest pest species, such as bark beetles (Coleoptera: Curculionidae, Scolytinae), and their host trees. Normally breeding mostly in broken or severely stressed spruce; at high population densities some bark beetle species can colonise and kill healthy trees on scales ranging from single trees in a stand to multi-annual landscape-wide outbreaks. In Eurasia, the largest outbreaks are caused by the spruce bark beetle, Ips typographus (Linnaeus), which is common and shares a wide distribution with its main host, Norway spruce (Picea abies Karst.). A large literature is now available, from which this review aims to synthesize research relevant for the population dynamics of I. typographus and co-occurring species under changing conditions. We find that spruce bark beetle population dynamics tend to be metastable, but that mixed-species and age-heterogeneous forests with good site-matching tend to be less susceptible to large-scale outbreaks. While large accumulations of logs should be removed and/or debarked before the next swarming period, intensive removal of all coarse dead wood may be counterproductive, as it reduces the diversity of predators that in some areas may play a role in keeping I. typographus populations below the outbreak threshold, and sanitary logging frequently causes edge effects and root damage, reducing the resistance of remaining trees. It is very hard to predict the outcome of interspecific interactions due to invading beetle species or I. typographus establishing outside its current range, as they can be of varying sign and strength and may fluctuate depending on environmental factors and population phase. Most research indicates that beetle outbreaks will increase in frequency and magnitude as temperature, wind speed and

  11. Population dynamics of three songbird species in a nestbox population in Central Europe show effects of density, climate and competitive interactions

    NARCIS (Netherlands)

    Smallegange, I.M.; van der Meer, J.; Fiedler, W.

    2011-01-01

    Unravelling the contributions of density-dependent and density-independent factors in determining species population dynamics is a challenge, especially if the two factors interact. One approach is to apply stochastic population models to long-term data, yet few studies have included interactions

  12. Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

    Science.gov (United States)

    Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

    2018-02-01

    The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

  13. Using citizen science butterfly counts to predict species population trends.

    Science.gov (United States)

    Dennis, Emily B; Morgan, Byron J T; Brereton, Tom M; Roy, David B; Fox, Richard

    2017-12-01

    Citizen scientists are increasingly engaged in gathering biodiversity information, but trade-offs are often required between public engagement goals and reliable data collection. We compared population estimates for 18 widespread butterfly species derived from the first 4 years (2011-2014) of a short-duration citizen science project (Big Butterfly Count [BBC]) with those from long-running, standardized monitoring data collected by experienced observers (U.K. Butterfly Monitoring Scheme [UKBMS]). BBC data are gathered during an annual 3-week period, whereas UKBMS sampling takes place over 6 months each year. An initial comparison with UKBMS data restricted to the 3-week BBC period revealed that species population changes were significantly correlated between the 2 sources. The short-duration sampling season rendered BBC counts susceptible to bias caused by interannual phenological variation in the timing of species' flight periods. The BBC counts were positively related to butterfly phenology and sampling effort. Annual estimates of species abundance and population trends predicted from models including BBC data and weather covariates as a proxy for phenology correlated significantly with those derived from UKBMS data. Overall, citizen science data obtained using a simple sampling protocol produced comparable estimates of butterfly species abundance to data collected through standardized monitoring methods. Although caution is urged in extrapolating from this U.K. study of a small number of common, conspicuous insects, we found that mass-participation citizen science can simultaneously contribute to public engagement and biodiversity monitoring. Mass-participation citizen science is not an adequate replacement for standardized biodiversity monitoring but may extend and complement it (e.g., through sampling different land-use types), as well as serving to reconnect an increasingly urban human population with nature. © 2017 The Authors. Conservation Biology published

  14. The role of demography, intra-species variation, and species distribution models in species’ projections under climate change

    DEFF Research Database (Denmark)

    Swab, Rebecca Marie; Regan, Helen M.; Matthies, Diethart

    2015-01-01

    Organisms are projected to shift their distribution ranges under climate change. The typical way to assess range shifts is by species distribution models (SDMs), which predict species’ responses to climate based solely on projected climatic suitability. However, life history traits can impact...... species’ responses to shifting habitat suitability. Additionally, it remains unclear if differences in vital rates across populations within a species can offset or exacerbate the effects of predicted changes in climatic suitability on population viability. In order to obtain a fuller understanding...... of the response of one species to projected climatic changes, we coupled demographic processes with predicted changes in suitable habitat for the monocarpic thistle Carlina vulgaris across northern Europe. We first developed a life history model with species-specific average fecundity and survival rates...

  15. Founding population size of an aquatic invasive species

    Science.gov (United States)

    Kalinowski, Steven T.; Muhlfeld, Clint C.; Guy, Christopher S.; Benjamin Cox,

    2010-01-01

    Non-native species of fish threaten native fishes throughout North America, and in the Rocky Mountains, introduced populations of lake trout threaten native populations of bull trout. Effective management of lake trout and other exotic species require understanding the dynamics of invasion in order to either suppress non-native populations or to prevent their spread. In this study, we used microsatellite genetic data to estimate the number of lake trout that invaded a population of bull trout in Swan Lake, MT. Examination of genetic diversity and allele frequencies within the Swan Lake populations showed that most of the genes in the lake trout population are descended from two founders. This emphasizes the importance of preventing even a few lake trout from colonizing new territory.

  16. Integrated Spectral Energy Distributions and Absorption Feature Indices of Single Stellar Populations

    OpenAIRE

    Zhang, Fenghui; Han, Zhanwen; Li, Lifang; Hurley, Jarrod R.

    2004-01-01

    Using evolutionary population synthesis, we present integrated spectral energy distributions and absorption-line indices defined by the Lick Observatory image dissector scanner (referred to as Lick/IDS) system, for an extensive set of instantaneous burst single stellar populations (SSPs). The ages of the SSPs are in the range 1-19 Gyr and the metallicities [Fe/H] are in the range -2.3 - 0.2. Our models use the rapid single stellar evolution algorithm of Hurley, Pols and Tout for the stellar e...

  17. Stimulus-dependent maximum entropy models of neural population codes.

    Directory of Open Access Journals (Sweden)

    Einat Granot-Atedgi

    Full Text Available Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME model-a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population.

  18. A simple model for skewed species-lifetime distributions

    KAUST Repository

    Murase, Yohsuke

    2010-06-11

    A simple model of a biological community assembly is studied. Communities are assembled by successive migrations and extinctions of species. In the model, species are interacting with each other. The intensity of the interaction between each pair of species is denoted by an interaction coefficient. At each time step, a new species is introduced to the system with randomly assigned interaction coefficients. If the sum of the coefficients, which we call the fitness of a species, is negative, the species goes extinct. The species-lifetime distribution is found to be well characterized by a stretched exponential function with an exponent close to 1/2. This profile agrees not only with more realistic population dynamics models but also with fossil records. We also find that an age-independent and inversely diversity-dependent mortality, which is confirmed in the simulation, is a key mechanism accounting for the distribution. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

  19. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.

    Science.gov (United States)

    Hess, Jon E; Campbell, Nathan R; Close, David A; Docker, Margaret F; Narum, Shawn R

    2013-06-01

    Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow. © 2012 John Wiley & Sons Ltd.

  20. Recovery of an endangered butterfly species, Shijimiaeoides divinus, population at Azumino in Nagano Prefecture, Japan

    OpenAIRE

    KODA, Keiko

    2014-01-01

    The large shijimi blue, Shijimiaeoides divinus, is a grassland lycaenid butterfly classified as an endangered species by the Ministry of Environment. In this study, I report on the life history of S. divinus barine and provide new data on the recovery of the natural population in Azumino. This butterfly is single-breeded with the adults usually appearing from late May to early June in Nagano Prefecture. Only three populations of S. divinus barine are maintained in Nagano Prefecture by several...

  1. Repeatability and reproducibility of Population Viability Analysis (PVA and the implications for threatened species management

    Directory of Open Access Journals (Sweden)

    Clare Morrison

    2016-08-01

    Full Text Available Conservation triage focuses on prioritizing species, populations or habitats based on urgency, biodiversity benefits, recovery potential as well as cost. Population Viability Analysis (PVA is frequently used in population focused conservation prioritizations. The critical nature of many of these management decisions requires that PVA models are repeatable and reproducible to reliably rank species and/or populations quantitatively. This paper assessed the repeatability and reproducibility of a subset of previously published PVA models. We attempted to rerun baseline models from 90 publicly available PVA studies published between 2000-2012 using the two most common PVA modelling software programs, VORTEX and RAMAS-GIS. Forty percent (n = 36 failed, 50% (45 were both repeatable and reproducible, and 10% (9 had missing baseline models. Repeatability was not linked to taxa, IUCN category, PVA program version used, year published or the quality of publication outlet, suggesting that the problem is systemic within the discipline. Complete and systematic presentation of PVA parameters and results are needed to ensure that the scientific input into conservation planning is both robust and reliable, thereby increasing the chances of making decisions that are both beneficial and defensible. The implications for conservation triage may be far reaching if population viability models cannot be reproduced with confidence, thus undermining their intended value.

  2. Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels.

    Science.gov (United States)

    Settepani, V; Schou, M F; Greve, M; Grinsted, L; Bechsgaard, J; Bilde, T

    2017-08-01

    Across several animal taxa, the evolution of sociality involves a suite of characteristics, a "social syndrome," that includes cooperative breeding, reproductive skew, primary female-biased sex ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genomewide diversity in spider species that differ in level of sociality, reproductive skew and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within-population diversity were sixfold to 10-fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genomewide diversity, likely to limit their evolutionary potential. © 2017 John Wiley & Sons Ltd.

  3. Modeling population dynamics and economic growth as competing species. An application to CO2 global emissions

    International Nuclear Information System (INIS)

    Puliafito, Salvador Enrique; Puliafito, Jose Luis; Grand, Mariana Conte

    2008-01-01

    Since the beginning of the last century the world is experiencing an important demographic transition, which will probably impact on economic growth. Many demographers and social scientists are trying to understand the key drivers of such transition as well as its profound implications. A correct understanding will help to predict other important trends of the world primary energy demand and the carbon emission to the atmosphere, which may be leading to an important climate change. This paper proposes a set of coupled differential equations to describe the changes of population, gross domestic product, primary energy consumption and carbon emissions, modeled as competing species as in Lotka-Volterra prey-predator relations. The predator-prey model is well known in the biological, ecological and environmental literature and has also been applied successfully in other fields. This model proposes a new and simple conceptual explanation of the interactions and feedbacks among the principal driving forces leading to the present transition. The estimated results for the temporal evolution of world population, gross domestic product, primary energy consumption and carbon emissions are calculated from year 1850 to year 2150. The calculated scenarios are in good agreement with common world data and projections for the next 100 years. (author)

  4. Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp. in the Nicaraguan crater lakes

    Directory of Open Access Journals (Sweden)

    Meyer Axel

    2010-10-01

    Full Text Available Abstract Background Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites. We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios. Results We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s of each crater lake differs, although most of them occurred more (probably much more recently than 20,000 years ago. Conclusion The

  5. Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes.

    Science.gov (United States)

    Barluenga, Marta; Meyer, Axel

    2010-10-26

    Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios. We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old) and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s) of each crater lake differs, although most of them occurred more (probably much more) recently than 20,000 years ago. The genetic differentiation of the crater lake populations

  6. Population pharmacokinetics of recombinant coagulation factor VIII-SingleChain in patients with severe hemophilia A.

    Science.gov (United States)

    Zhang, Y; Roberts, J; Tortorici, M; Veldman, A; St Ledger, K; Feussner, A; Sidhu, J

    2017-06-01

    Essentials rVIII-SingleChain is a unique recombinant factor VIII (FVIII) molecule. A population pharmacokinetic model was based on FVIII activity of severe hemophilia A patients. The model was used to simulate factor VIII activity-time profiles for various dosing scenarios. The model supports prolonged dosing of rVIII-SingleChain with intervals of up to twice per week. Background Single-chain recombinant coagulation factor VIII (rVIII-SingleChain) is a unique recombinant coagulation factor VIII molecule. Objectives To: (i) characterize the population pharmacokinetics (PK) of rVIII-SingleChain in patients with severe hemophilia A; (ii) identify correlates of variability in rVIII-SingleChain PK; and (iii) simulate various dosing scenarios of rVIII-SingleChain. Patients/Methods A population PK model was developed, based on FVIII activity levels of 130 patients with severe hemophilia A (n = 91 for ≥ 12-65 years; n = 39 for  85% and > 93% of patients were predicted to maintain FVIII activity level above 1 IU dL -1 , at all times with three-times-weekly dosing (given on days 0, 2, and 4.5) at the lowest (20 IU kg -1 ) and highest (50 IU kg -1 ) doses, respectively. For twice weekly dosing (days 0 and 3.5) of 50 IU kg -1 rVIII-SingleChain, 62-80% of patients across all ages were predicted to maintain a FVIII activity level above 1 IU dL -1 at day 7. Conclusions The population PK model adequately characterized rVIII-SingleChain PK, and the model can be utilized to simulate FVIII activity-time profiles for various dosing scenarios. © 2017 The Authors. Journal of Thrombosis and Haemostasis published by Wiley Periodicals, Inc. on behalf of International Society on Thrombosis and Haemostasis.

  7. A comparative approach using ecotoxicological methods from single-species bioassays to model ecosystems.

    Science.gov (United States)

    Haegerbaeumer, Arne; Höss, Sebastian; Ristau, Kai; Claus, Evelyn; Möhlenkamp, Christel; Heininger, Peter; Traunspurger, Walter

    2016-12-01

    Soft sediments are often hotspots of chemical contamination, and a thorough ecotoxicological assessment of this habitat can help to identify the causes of stress and to improve the health of the respective ecosystems. As an important component of the ecologically relevant meiobenthic fauna, nematodes can be used for sediment assessments, with various assay tools ranging from single-species toxicity tests to field studies. In the present study, microcosms containing sediment were used to investigate direct and indirect effects of zinc on natural nematode assemblages, and acute community toxicity tests considering only direct toxicity were conducted. The responses of the various freshwater nematode species in both approaches were compared with those of Caenorhabditis elegans, determined in standardized tests (ISO 10872). At a median lethal concentration (LC50) of 20 mg Zn/L, C. elegans represented the median susceptibility of 15 examined nematode species examined in the acute community toxicity tests. In the microcosms, Zn affected the nematodes dose-dependently, with changes in species composition first detected at 13 mg Zn/kg to 19 mg Zn/kg sediment dry weight. The observed species sensitivities in the microcosms corresponded better to field observations than to the results of the acute community toxicity tests. Environ Toxicol Chem 2016;35:2987-2997. © 2016 SETAC. © 2016 SETAC.

  8. Placing invasive species management in a spatiotemporal context.

    Science.gov (United States)

    Baker, Christopher M; Bode, Michael

    2016-04-01

    Invasive species are a worldwide issue, both ecologically and economically. A large body of work focuses on various aspects of invasive species control, including how to allocate control efforts to eradicate an invasive population as cost effectively as possible: There are a diverse range of invasive species management problems, and past mathematical analyses generally focus on isolated examples, making it hard to identify and understand parallels between the different contexts. In this study, we use a single spatiotemporal model to tackle the problem of allocating control effort for invasive species when suppressing an island invasive species, and for long-term spatial suppression projects. Using feral cat suppression as an illustrative example, we identify the optimal resource allocation for island and mainland suppression projects. Our results demonstrate how using a single model to solve different problems reveals similar characteristics of the solutions in different scenarios. As well as illustrating the insights offered by linking problems through a spatiotemporal model, we also derive novel and practically applicable results for our case studies. For temporal suppression projects on islands, we find that lengthy projects are more cost effective and that rapid control projects are only economically cost effective when population growth rates are high or diminishing returns on control effort are low. When suppressing invasive species around conservation assets (e.g., national parks or exclusion fences), we find that the size of buffer zones should depend on the ratio of the species growth and spread rate.

  9. Single bumps in a 2-population homogenized neuronal network model

    Science.gov (United States)

    Kolodina, Karina; Oleynik, Anna; Wyller, John

    2018-05-01

    We investigate existence and stability of single bumps in a homogenized 2-population neural field model, when the firing rate functions are given by the Heaviside function. The model is derived by means of the two-scale convergence technique of Nguetseng in the case of periodic microvariation in the connectivity functions. The connectivity functions are periodically modulated in both the synaptic footprint and in the spatial scale. The bump solutions are constructed by using a pinning function technique for the case where the solutions are independent of the local variable. In the weakly modulated case the generic picture consists of two bumps (one narrow and one broad bump) for each admissible set of threshold values for firing. In addition, a new threshold value regime for existence of bumps is detected. Beyond the weakly modulated regime the number of bumps depends sensitively on the degree of heterogeneity. For the latter case we present a configuration consisting of three coexisting bumps. The linear stability of the bumps is studied by means of the spectral properties of a Fredholm integral operator, block diagonalization of this operator and the Fourier decomposition method. In the weakly modulated regime, one of the bumps is unstable for all relative inhibition times, while the other one is stable for small and moderate values of this parameter. The latter bump becomes unstable as the relative inhibition time exceeds a certain threshold. In the case of the three coexisting bumps detected in the regime of finite degree of heterogeneity, we have at least one stable bump (and maximum two stable bumps) for small and moderate values of the relative inhibition time.

  10. A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

    Science.gov (United States)

    Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

    2012-09-01

    Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

  11. Modelling the Dynamics of an Aedes albopictus Population

    Directory of Open Access Journals (Sweden)

    Thomas Anung Basuki

    2010-08-01

    Full Text Available We present a methodology for modelling population dynamics with formal means of computer science. This allows unambiguous description of systems and application of analysis tools such as simulators and model checkers. In particular, the dynamics of a population of Aedes albopictus (a species of mosquito and its modelling with the Stochastic Calculus of Looping Sequences (Stochastic CLS are considered. The use of Stochastic CLS to model population dynamics requires an extension which allows environmental events (such as changes in the temperature and rainfalls to be taken into account. A simulator for the constructed model is developed via translation into the specification language Maude, and used to compare the dynamics obtained from the model with real data.

  12. The role of advection in a two-species competition model

    CERN Document Server

    Averill, Isabel; Lou, Yuan

    2017-01-01

    The effects of weak and strong advection on the dynamics of reaction-diffusion models have long been studied. In contrast, the role of intermediate advection remains poorly understood. For example, concentration phenomena can occur when advection is strong, providing a mechanism for the coexistence of multiple populations, in contrast with the situation of weak advection where coexistence may not be possible. The transition of the dynamics from weak to strong advection is generally difficult to determine. In this work the authors consider a mathematical model of two competing populations in a spatially varying but temporally constant environment, where both species have the same population dynamics but different dispersal strategies: one species adopts random dispersal, while the dispersal strategy for the other species is a combination of random dispersal and advection upward along the resource gradient. For any given diffusion rates the authors consider the bifurcation diagram of positive steady states by u...

  13. Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data.

    Science.gov (United States)

    Tang, Cuong Q; Humphreys, Aelys M; Fontaneto, Diego; Barraclough, Timothy G; Paradis, Emmanuel

    2014-10-01

    Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.

  14. Indicator Species Population Monitoring in Antarctica with Uav

    Science.gov (United States)

    Zmarz, A.; Korczak-Abshire, M.; Storvold, R.; Rodzewicz, M.; Kędzierska, I.

    2015-08-01

    A program to monitor bird and pinniped species in the vicinity of Arctowski Station, King George Island, South Shetlands, Antarctica, has been conducted over the past 38 years. Annual monitoring of these indicator species includes estimations of breeding population sizes of three Pygoscelis penguin species: Adélie, gentoo and chinstrap. Six penguin colonies situated on the western shores of two bays: Admiralty and King George are investigated. To study changes in penguin populations Unmanned Aerial Vehicles were used for the first time in the 2014/15 austral summer season. During photogrammetric flights the high-resolution images of eight penguin breeding colonies were taken. Obtained high resolution images were used for estimation of breeding population size and compared with the results of measurements taken at the same time from the ground. During this Antarctic expedition eight successful photogrammetry missions (total distance 1500 km) were performed. Images were taken with digital SLR Canon 700D, Nikon D5300, Nikon D5100 with a 35mm objective lens. Flights altitude at 350 - 400 AGL, allowed images to be taken with a resolution GSD (ground sample distance) less than 5 cm. The Image J software analysis method was tested to provide automatic population estimates from obtained images. The use of UAV for monitoring of indicator species, enabled data acquisition from areas inaccessible by ground methods.

  15. INDICATOR SPECIES POPULATION MONITORING IN ANTARCTICA WITH UAV

    Directory of Open Access Journals (Sweden)

    A. Zmarz

    2015-08-01

    Full Text Available A program to monitor bird and pinniped species in the vicinity of Arctowski Station, King George Island, South Shetlands, Antarctica, has been conducted over the past 38 years. Annual monitoring of these indicator species includes estimations of breeding population sizes of three Pygoscelis penguin species: Adélie, gentoo and chinstrap. Six penguin colonies situated on the western shores of two bays: Admiralty and King George are investigated. To study changes in penguin populations Unmanned Aerial Vehicles were used for the first time in the 2014/15 austral summer season. During photogrammetric flights the high-resolution images of eight penguin breeding colonies were taken. Obtained high resolution images were used for estimation of breeding population size and compared with the results of measurements taken at the same time from the ground. During this Antarctic expedition eight successful photogrammetry missions (total distance 1500 km were performed. Images were taken with digital SLR Canon 700D, Nikon D5300, Nikon D5100 with a 35mm objective lens. Flights altitude at 350 – 400 AGL, allowed images to be taken with a resolution GSD (ground sample distance less than 5 cm. The Image J software analysis method was tested to provide automatic population estimates from obtained images. The use of UAV for monitoring of indicator species, enabled data acquisition from areas inaccessible by ground methods.

  16. Using empirical models of species colonization under multiple threatening processes to identify complementary threat-mitigation strategies.

    Science.gov (United States)

    Tulloch, Ayesha I T; Mortelliti, Alessio; Kay, Geoffrey M; Florance, Daniel; Lindenmayer, David

    2016-08-01

    Approaches to prioritize conservation actions are gaining popularity. However, limited empirical evidence exists on which species might benefit most from threat mitigation and on what combination of threats, if mitigated simultaneously, would result in the best outcomes for biodiversity. We devised a way to prioritize threat mitigation at a regional scale with empirical evidence based on predicted changes to population dynamics-information that is lacking in most threat-management prioritization frameworks that rely on expert elicitation. We used dynamic occupancy models to investigate the effects of multiple threats (tree cover, grazing, and presence of an hyperaggressive competitor, the Noisy Miner (Manorina melanocephala) on bird-population dynamics in an endangered woodland community in southeastern Australia. The 3 threatening processes had different effects on different species. We used predicted patch-colonization probabilities to estimate the benefit to each species of removing one or more threats. We then determined the complementary set of threat-mitigation strategies that maximized colonization of all species while ensuring that redundant actions with little benefit were avoided. The single action that resulted in the highest colonization was increasing tree cover, which increased patch colonization by 5% and 11% on average across all species and for declining species, respectively. Combining Noisy Miner control with increasing tree cover increased species colonization by 10% and 19% on average for all species and for declining species respectively, and was a higher priority than changing grazing regimes. Guidance for prioritizing threat mitigation is critical in the face of cumulative threatening processes. By incorporating population dynamics in prioritization of threat management, our approach helps ensure funding is not wasted on ineffective management programs that target the wrong threats or species. © 2016 Society for Conservation Biology.

  17. Benchmarking novel approaches for modelling species range dynamics.

    Science.gov (United States)

    Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

    2016-08-01

    Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches

  18. Effects of white-nose syndrome on regional population patterns of 3 hibernating bat species.

    Science.gov (United States)

    Ingersoll, Thomas E; Sewall, Brent J; Amelon, Sybill K

    2016-10-01

    Hibernating bats have undergone severe recent declines across the eastern United States, but the cause of these regional-scale declines has not been systematically evaluated. We assessed the influence of white-nose syndrome (an emerging bat disease caused by the fungus Pseudogymnoascus destructans, formerly Geomyces destructans) on large-scale, long-term population patterns in the little brown myotis (Myotis lucifugus), the northern myotis (Myotis septentrionalis), and the tricolored bat (Perimyotis subflavus). We modeled population trajectories for each species on the basis of an extensive data set of winter hibernacula counts of more than 1 million individual bats from a 4-state region over 13 years and with data on locations of hibernacula and first detections of white-nose syndrome at each hibernaculum. We used generalized additive mixed models to determine population change relative to expectations, that is, how population trajectories differed with a colony's infection status, how trajectories differed with distance from the point of introduction of white-nose syndrome, and whether declines were concordant with first local observation of the disease. Population trajectories in all species met at least one of the 3 expectations, but none met all 3. Our results suggest, therefore, that white-nose syndrome has affected regional populations differently than was previously understood and has not been the sole cause of declines. Specifically, our results suggest that in some areas and species, threats other than white-nose syndrome are also contributing to population declines, declines linked to white-nose syndrome have spread across large geographic areas with unexpected speed, and the disease or other threats led to declines in bat populations for years prior to disease detection. Effective conservation will require further research to mitigate impacts of white-nose syndrome, renewed attention to other threats to bats, and improved surveillance efforts to ensure

  19. Population dynamics along a primary succession gradient: do alpine species fit into demographic succession theory?

    Science.gov (United States)

    Marcante, Silvia; Winkler, Eckart; Erschbamer, Brigitta

    2009-05-01

    Understanding processes and mechanisms governing changes in plant species along primary successions has been of major importance in ecology. However, to date hardly any studies have focused on the complete life cycle of species along a successional gradient, comparing pioneer, early and late-successional species. In this study it is hypothesized that pioneer species should initially have a population growth rate, lambda, greater than one with high fecundity rates, and declining growth rates when they are replaced by late-successional species. Populations of late-successional species should also start, at the mid-successional stage (when pioneer species are declining), with growth rates greater than one and arrive at rates equal to one at the late successional stage, mainly due to higher survival rates that allow these species to persist for a long time. The demography of pioneer- (Saxifraga aizoides), early (Artemisia genipi) and late-successional species (Anthyllis vulneraria ssp. alpicola) was investigated together with that of a ubiquitous species (Poa alpina) along the Rotmoos glacier foreland (2300-2400 m a.s.l., Central Alps, Austria) over 3 years. A matrix modelling approach was used to compare the main demographic parameters. Elasticity values were plotted in a demographic triangle using fecundity, individual growth and survival as vital rates contributing to the population growth rates. The results largely confirmed the predictions for population growth rates during succession. However, high survival rates of larger adults characterized all species, regardless of where they were growing along the succession. At the pioneer site, high mortality rates of seedlings, plantlets and young individuals were recorded. Fecundity was found to be of minor relevance everywhere, but it was nevertheless sufficient to increase or maintain the population sizes. Demographically, all the species over all sites behaved like late-successional or climax species in secondary

  20. Population-expression models of immune response

    International Nuclear Information System (INIS)

    Stromberg, Sean P; Antia, Rustom; Nemenman, Ilya

    2013-01-01

    The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenotype to an effector phenotype which controls the pathogen, and subsequently to a memory phenotype that is maintained and responsible for long-term protection. The expansion and the differentiation have been considered largely independently. Changes in cell populations are typically described using ecologically based ordinary differential equation models. In contrast, differentiation of single cells is studied within systems biology and is frequently modeled by considering changes in gene and protein expression in individual cells. Recent advances in experimental systems biology make available for the first time data to allow the coupling of population and high dimensional expression data of immune cells during infections. Here we describe and develop population-expression models which integrate these two processes into systems biology on the multicellular level. When translated into mathematical equations, these models result in non-conservative, non-local advection-diffusion equations. We describe situations where the population-expression approach can make correct inference from data while previous modeling approaches based on common simplifying assumptions would fail. We also explore how model reduction techniques can be used to build population-expression models, minimizing the complexity of the model while keeping the essential features of the system. While we consider problems in immunology in this paper, we expect population-expression models to be more broadly applicable. (paper)

  1. A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

    Science.gov (United States)

    Buckley, Ralf C; Castley, J Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C; Steven, Rochelle

    2012-01-01

    Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.

  2. A Population Accounting Approach to Assess Tourism Contributions to Conservation of IUCN-Redlisted Mammal Species

    Science.gov (United States)

    Buckley, Ralf C.; Castley, J. Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C.; Steven, Rochelle

    2012-01-01

    Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥5% for over half of the species where relevant data exist, ≥15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species. PMID:22984467

  3. A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

    Directory of Open Access Journals (Sweden)

    Ralf C Buckley

    Full Text Available Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.

  4. Using temporal sampling to improve attribution of source populations for invasive species.

    Directory of Open Access Journals (Sweden)

    Sharyn J Goldstien

    Full Text Available Numerous studies have applied genetic tools to the identification of source populations and transport pathways for invasive species. However, there are many gaps in the knowledge obtained from such studies because comprehensive and meaningful spatial sampling to meet these goals is difficult to achieve. Sampling populations as they arrive at the border should fill the gaps in source population identification, but such an advance has not yet been achieved with genetic data. Here we use previously acquired genetic data to assign new incursions as they invade populations within New Zealand ports and marinas. We also investigated allelelic frequency change in these recently established populations over a two-year period, and assessed the effect of temporal genetic sampling on our ability to assign new incursions to their population of source. We observed shifts in the allele frequencies among populations, as well as the complete loss of some alleles and the addition of alleles novel to New Zealand, within these recently established populations. There was no significant level of genetic differentiation observed in our samples between years, and the use of these temporal data did alter the assignment probability of new incursions. Our study further suggests that new incursions can add genetic variation to the population in a single introduction event as the founders themselves are often more genetically diverse than theory initially predicted.

  5. ALIEN SPECIES: THEIR ROLE IN AMPHIBIAN POPULATION DECLINES AND RESTORATION

    Science.gov (United States)

    Alien species (also referred to as exotic, invasive, introduced, or normative species) have been implicated as causal agents in population declines of many amphibian species. Herein, we evaluate the relative contributions of alien species and other factors in adversely affecting ...

  6. Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers.

    Directory of Open Access Journals (Sweden)

    Shanmugapriya Arumugasundaram

    Full Text Available Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r(2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r(2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.

  7. Composite spectral functions for solving Volterra's population model

    International Nuclear Information System (INIS)

    Ramezani, M.; Razzaghi, M.; Dehghan, M.

    2007-01-01

    An approximate method for solving Volterra's population model for population growth of a species in a closed system is proposed. Volterra's model is a nonlinear integro-differential equation, where the integral term represents the effect of toxin. The approach is based upon composite spectral functions approximations. The properties of composite spectral functions consisting of few terms of orthogonal functions are presented and are utilized to reduce the solution of the Volterra's model to the solution of a system of algebraic equations. The method is easy to implement and yields very accurate result

  8. Impact of environmental colored noise in single-species population dynamics

    Science.gov (United States)

    Spanio, Tommaso; Hidalgo, Jorge; Muñoz, Miguel A.

    2017-10-01

    Variability on external conditions has important consequences for the dynamics and the organization of biological systems. In many cases, the characteristic timescale of environmental changes as well as their correlations play a fundamental role in the way living systems adapt and respond to it. A proper mathematical approach to understand population dynamics, thus, requires approaches more refined than, e.g., simple white-noise approximations. To shed further light onto this problem, in this paper we propose a unifying framework based on different analytical and numerical tools available to deal with "colored" environmental noise. In particular, we employ a "unified colored noise approximation" to map the original problem into an effective one with white noise, and then we apply a standard path integral approach to gain analytical understanding. For the sake of specificity, we present our approach using as a guideline a variation of the contact process—which can also be seen as a birth-death process of the Malthus-Verhulst class—where the propagation or birth rate varies stochastically in time. Our approach allows us to tackle in a systematic manner some of the relevant questions concerning population dynamics under environmental variability, such as determining the stationary population density, establishing the conditions under which a population may become extinct, and estimating extinction times. We focus on the emerging phase diagram and its possible phase transitions, underlying how these are affected by the presence of environmental noise time-correlations.

  9. Assessing Model Characterization of Single Source ...

    Science.gov (United States)

    Aircraft measurements made downwind from specific coal fired power plants during the 2013 Southeast Nexus field campaign provide a unique opportunity to evaluate single source photochemical model predictions of both O3 and secondary PM2.5 species. The model did well at predicting downwind plume placement. The model shows similar patterns of an increasing fraction of PM2.5 sulfate ion to the sum of SO2 and PM2.5 sulfate ion by distance from the source compared with ambient based estimates. The model was less consistent in capturing downwind ambient based trends in conversion of NOX to NOY from these sources. Source sensitivity approaches capture near-source O3 titration by fresh NO emissions, in particular subgrid plume treatment. However, capturing this near-source chemical feature did not translate into better downwind peak estimates of single source O3 impacts. The model estimated O3 production from these sources but often was lower than ambient based source production. The downwind transect ambient measurements, in particular secondary PM2.5 and O3, have some level of contribution from other sources which makes direct comparison with model source contribution challenging. Model source attribution results suggest contribution to secondary pollutants from multiple sources even where primary pollutants indicate the presence of a single source. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates data, deci

  10. Evaluating models of population process in a threatened population of Steller’s eiders: A retrospective approach

    Science.gov (United States)

    Dunham, Kylee; Grand, James B.

    2016-10-11

    The Alaskan breeding population of Steller’s eiders (Polysticta stelleri) was listed as threatened under the Endangered Species Act in 1997 in response to perceived declines in abundance throughout their breeding and nesting range. Aerial surveys suggest the breeding population is small and highly variable in number, with zero birds counted in 5 of the last 25 years. Research was conducted to evaluate competing population process models of Alaskan-breeding Steller’s eiders through comparison of model projections to aerial survey data. To evaluate model efficacy and estimate demographic parameters, a Bayesian state-space modeling framework was used and each model was fit to counts from the annual aerial surveys, using sequential importance sampling and resampling. The results strongly support that the Alaskan breeding population experiences population level nonbreeding events and is open to exchange with the larger Russian-Pacific breeding population. Current recovery criteria for the Alaskan breeding population rely heavily on the ability to estimate population viability. The results of this investigation provide an informative model of the population process that can be used to examine future population states and assess the population in terms of the current recovery and reclassification criteria.

  11. High prices for rare species can drive large populations extinct: the anthropogenic Allee effect revisited.

    Science.gov (United States)

    Holden, Matthew H; McDonald-Madden, Eve

    2017-09-21

    Consumer demand for plant and animal products threatens many populations with extinction. The anthropogenic Allee effect (AAE) proposes that such extinctions can be caused by prices for wildlife products increasing with species rarity. This price-rarity relationship creates financial incentives to extract the last remaining individuals of a population, despite higher search and harvest costs. The AAE has become a standard approach for conceptualizing the threat of economic markets on endangered species. Despite its potential importance for conservation, AAE theory is based on a simple graphical model with limited analysis of possible population trajectories. By specifying a general class of functions for price-rarity relationships, we show that the classic theory can understate the risk of species extinction. AAE theory proposes that only populations below a critical Allee threshold will go extinct due to increasing price-rarity relationships. Our analysis shows that this threshold can be much higher than the original theory suggests, depending on initial harvest effort. More alarmingly, even species with population sizes above this Allee threshold, for which AAE predicts persistence, can be destined to extinction. Introducing even a minimum price for harvested individuals, close to zero, can cause large populations to cross the classic anthropogenic Allee threshold on a trajectory towards extinction. These results suggest that traditional AAE theory may give a false sense of security when managing large harvested populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. From single-species advice to mixed-species management: taking the next step

    DEFF Research Database (Denmark)

    Vinther, Morten; Reeves, S.A.; Patterson, K.R.

    2004-01-01

    Fishery management advice has traditionally been given on a stock-by-stock basis. Recent problems in implementing this advice, particularly for the demersal fisheries of the North Sea, have highlighted the limitations of the approach. In the long term, it would be desirable to give advice...... that accounts for mixed-fishery effects, but in the short term there is a need for approaches to resolve the conflicting management advice for different species within the same fishery, and to generate catch or effort advice that accounts for the mixed-species nature of the fishery. This paper documents...... a recent approach used to address these problems. The approach takes the single-species advice for each species in the fishery as a starting point, then attempts to resolve it into consistent catch or effort advice using fleet-disaggregated catch forecasts in combination with explicitly stated management...

  13. Understanding the formation and evolution of early-type galaxies based on newly developed single-burst stellar population synthesis models in the infrared

    Science.gov (United States)

    Roeck, Benjamin

    2015-12-01

    The detailed study of the different stellar populations which can be observed in galaxies is one of the most promising methods to shed light on the evolutionary histories of galaxies. So far, stellar population analysis has been carried out mainly in the optical wavelength range. The infrared spectral range, on the other hand, has been poorly studied so far, although it provides very important insights, particularly into the cooler stellar populations which are present in galaxies. However, in the last years, space telescopes like the Spitzer Space Telescope or the Wide-field Infrared Survey Explorer and instruments like the spectrograph X-Shooter on the Very Large Telescope have collected more and more photometric and spectroscopic data in this wavelength range. In order to analyze these observations, it is necessary to dispose of reliable and accurate stellar population models in the infrared. Only a small number of stellar population models in the infrared exist in the literature. They are mostly based on theoretical stellar libraries and very often cover only the near-infrared wavelength range at a rather low resolution. Hence, we developed new single-burst stellar population models between 8150 and 50000Å which are exclusively based on 180 spectra from the empirical Infrared Telescope Facility stellar library. We computed our single stellar population models for two different sets of isochrones and various types of initial mass functions of different slopes. Since the stars of the Infrared Telescope Facility library present only a limited coverage of the stellar atmospheric parameter space, our models are of sufficient quality only for ages larger than 1 Gyr and metallicities between [Fe/H] = 0.40 and 0.26. By combining our single stellar population models in the infrared with the extended medium-resolution Isaac Newton Telescope library of empirical spectra in the optical spectral range, we created the first single stellar population models covering the

  14. Deriving field-based species sensitivity distributions (f-SSDs) from stacked species distribution models (S-SDMs).

    Science.gov (United States)

    Schipper, Aafke M; Posthuma, Leo; de Zwart, Dick; Huijbregts, Mark A J

    2014-12-16

    Quantitative relationships between species richness and single environmental factors, also called species sensitivity distributions (SSDs), are helpful to understand and predict biodiversity patterns, identify environmental management options and set environmental quality standards. However, species richness is typically dependent on a variety of environmental factors, implying that it is not straightforward to quantify SSDs from field monitoring data. Here, we present a novel and flexible approach to solve this, based on the method of stacked species distribution modeling. First, a species distribution model (SDM) is established for each species, describing its probability of occurrence in relation to multiple environmental factors. Next, the predictions of the SDMs are stacked along the gradient of each environmental factor with the remaining environmental factors at fixed levels. By varying those fixed levels, our approach can be used to investigate how field-based SSDs for a given environmental factor change in relation to changing confounding influences, including for example optimal, typical, or extreme environmental conditions. This provides an asset in the evaluation of potential management measures to reach good ecological status.

  15. An individual-based probabilistic model for simulating fisheries population dynamics

    Directory of Open Access Journals (Sweden)

    Jie Cao

    2016-12-01

    Full Text Available The purpose of stock assessment is to support managers to provide intelligent decisions regarding removal from fish populations. Errors in assessment models may have devastating impacts on the population fitness and negative impacts on the economy of the resource users. Thus, accuracte estimations of population size, growth rates are critical for success. Evaluating and testing the behavior and performance of stock assessment models and assessing the consequences of model mis-specification and the impact of management strategies requires an operating model that accurately describe the dynamics of the target species, and can resolve spatial and seasonal changes. In addition, the most thorough evaluations of assessment models use an operating model that takes a different form than the assessment model. This paper presents an individual-based probabilistic model used to simulate the complex dynamics of populations and their associated fisheries. Various components of population dynamics are expressed as random Bernoulli trials in the model and detailed life and fishery histories of each individual are tracked over their life span. The simulation model is designed to be flexible so it can be used for different species and fisheries. It can simulate mixing among multiple stocks and link stock-recruit relationships to environmental factors. Furthermore, the model allows for flexibility in sub-models (e.g., growth and recruitment and model assumptions (e.g., age- or size-dependent selectivity. This model enables the user to conduct various simulation studies, including testing the performance of assessment models under different assumptions, assessing the impacts of model mis-specification and evaluating management strategies.

  16. Evolutionary dynamics of fluctuating populations with strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David

    2013-03-01

    Evolutionary game theory with finite interacting populations is receiving increased attention, including subtle phenomena associated with number fluctuations, i.e., ``genetic drift.'' Models of cooperation and competition often utilize a simplified Moran model, with a strictly fixed total population size. We explore a more general evolutionary model with independent fluctuations in the numbers of two distinct species, in a regime characterized by ``strong mutualism.'' The model has two absorbing states, each corresponding to fixation of one of the two species, and allows exploration of the interplay between growth, competition, and mutualism. When mutualism is favored, number fluctuations eventually drive the system away from a stable fixed point, characterized by cooperation, to one of the absorbing states. Well-mixed populations will thus be taken over by a single species in a finite time, despite the bias towards cooperation. We calculate both the fixation probability and the mean fixation time as a function of the initial conditions and carrying capacities in the strong mutualism regime, using the method of matched asymptotic expansions. Our results are compared to computer simulations.

  17. Predicting habitat suitability for rare plants at local spatial scales using a species distribution model.

    Science.gov (United States)

    Gogol-Prokurat, Melanie

    2011-01-01

    If species distribution models (SDMs) can rank habitat suitability at a local scale, they may be a valuable conservation planning tool for rare, patchily distributed species. This study assessed the ability of Maxent, an SDM reported to be appropriate for modeling rare species, to rank habitat suitability at a local scale for four edaphic endemic rare plants of gabbroic soils in El Dorado County, California, and examined the effects of grain size, spatial extent, and fine-grain environmental predictors on local-scale model accuracy. Models were developed using species occurrence data mapped on public lands and were evaluated using an independent data set of presence and absence locations on surrounding lands, mimicking a typical conservation-planning scenario that prioritizes potential habitat on unsurveyed lands surrounding known occurrences. Maxent produced models that were successful at discriminating between suitable and unsuitable habitat at the local scale for all four species, and predicted habitat suitability values were proportional to likelihood of occurrence or population abundance for three of four species. Unfortunately, models with the best discrimination (i.e., AUC) were not always the most useful for ranking habitat suitability. The use of independent test data showed metrics that were valuable for evaluating which variables and model choices (e.g., grain, extent) to use in guiding habitat prioritization for conservation of these species. A goodness-of-fit test was used to determine whether habitat suitability values ranked habitat suitability on a continuous scale. If they did not, a minimum acceptable error predicted area criterion was used to determine the threshold for classifying habitat as suitable or unsuitable. I found a trade-off between model extent and the use of fine-grain environmental variables: goodness of fit was improved at larger extents, and fine-grain environmental variables improved local-scale accuracy, but fine-grain variables

  18. Population genetics of Setaria viridis, a new model system.

    Science.gov (United States)

    Huang, Pu; Feldman, Maximilian; Schroder, Stephan; Bahri, Bochra A; Diao, Xianmin; Zhi, Hui; Estep, Matt; Baxter, Ivan; Devos, Katrien M; Kellogg, Elizabeth A

    2014-10-01

    An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a worldwide sample of more than 200 S. viridis accessions, using the genotyping-by-sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modelled demographic history and show signal of recent population decline in one subgroup. Finally, we show linkage disequilibrium decay is rapid (<45 kb) in our total sample and slow in genetic subgroups. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work including germplasm preservation, local adaptation, crossing designs and genomewide association studies. © 2014 John Wiley & Sons Ltd.

  19. An individual-based model for population viability analysis of humpback chub in Grand Canyon

    Science.gov (United States)

    Pine, William Pine; Healy, Brian; Smith, Emily Omana; Trammell, Melissa; Speas, Dave; Valdez, Rich; Yard, Mike; Walters, Carl; Ahrens, Rob; Vanhaverbeke, Randy; Stone, Dennis; Wilson, Wade

    2013-01-01

    We developed an individual-based population viability analysis model (females only) for evaluating risk to populations from catastrophic events or conservation and research actions. This model tracks attributes (size, weight, viability, etc.) for individual fish through time and then compiles this information to assess the extinction risk of the population across large numbers of simulation trials. Using a case history for the Little Colorado River population of Humpback Chub Gila cypha in Grand Canyon, Arizona, we assessed extinction risk and resiliency to a catastrophic event for this population and then assessed a series of conservation actions related to removing specific numbers of Humpback Chub at different sizes for conservation purposes, such as translocating individuals to establish other spawning populations or hatchery refuge development. Our results suggested that the Little Colorado River population is generally resilient to a single catastrophic event and also to removals of larvae and juveniles for conservation purposes, including translocations to establish new populations. Our results also suggested that translocation success is dependent on similar survival rates in receiving and donor streams and low emigration rates from recipient streams. In addition, translocating either large numbers of larvae or small numbers of large juveniles has generally an equal likelihood of successful population establishment at similar extinction risk levels to the Little Colorado River donor population. Our model created a transparent platform to consider extinction risk to populations from catastrophe or conservation actions and should prove useful to managers assessing these risks for endangered species such as Humpback Chub.

  20. Critical thresholds for eventual extinction in randomly disturbed population growth models.

    Science.gov (United States)

    Peckham, Scott D; Waymire, Edward C; De Leenheer, Patrick

    2018-02-16

    This paper considers several single species growth models featuring a carrying capacity, which are subject to random disturbances that lead to instantaneous population reduction at the disturbance times. This is motivated in part by growing concerns about the impacts of climate change. Our main goal is to understand whether or not the species can persist in the long run. We consider the discrete-time stochastic process obtained by sampling the system immediately after the disturbances, and find various thresholds for several modes of convergence of this discrete process, including thresholds for the absence or existence of a positively supported invariant distribution. These thresholds are given explicitly in terms of the intensity and frequency of the disturbances on the one hand, and the population's growth characteristics on the other. We also perform a similar threshold analysis for the original continuous-time stochastic process, and obtain a formula that allows us to express the invariant distribution for this continuous-time process in terms of the invariant distribution of the discrete-time process, and vice versa. Examples illustrate that these distributions can differ, and this sends a cautionary message to practitioners who wish to parameterize these and related models using field data. Our analysis relies heavily on a particular feature shared by all the deterministic growth models considered here, namely that their solutions exhibit an exponentially weighted averaging property between a function of the initial condition, and the same function applied to the carrying capacity. This property is due to the fact that these systems can be transformed into affine systems.

  1. Species distributions models in wildlife planning: agricultural policy and wildlife management in the great plains

    Science.gov (United States)

    Fontaine, Joseph J.; Jorgensen, Christopher; Stuber, Erica F.; Gruber, Lutz F.; Bishop, Andrew A.; Lusk, Jeffrey J.; Zach, Eric S.; Decker, Karie L.

    2017-01-01

    We know economic and social policy has implications for ecosystems at large, but the consequences for a given geographic area or specific wildlife population are more difficult to conceptualize and communicate. Species distribution models, which extrapolate species-habitat relationships across ecological scales, are capable of predicting population changes in distribution and abundance in response to management and policy, and thus, are an ideal means for facilitating proactive management within a larger policy framework. To illustrate the capabilities of species distribution modeling in scenario planning for wildlife populations, we projected an existing distribution model for ring-necked pheasants (Phasianus colchicus) onto a series of alternative future landscape scenarios for Nebraska, USA. Based on our scenarios, we qualitatively and quantitatively estimated the effects of agricultural policy decisions on pheasant populations across Nebraska, in specific management regions, and at wildlife management areas. 

  2. A single nucleotide polymorphism (SNP) assay for population ...

    African Journals Online (AJOL)

    A single nucleotide polymorphism (SNP) assay for population stratification test ... phenotypes and unlinked candidate loci in case-control and cohort studies of ... Key words: Chinese, Japanese, population stratification, ancestry informative ...

  3. Metapopulation modelling of riparian tree species persistence in river networks under climate change.

    Science.gov (United States)

    Van Looy, Kris; Piffady, Jérémy

    2017-11-01

    Floodplain landscapes are highly fragmented by river regulation resulting in habitat degradation and flood regime perturbation, posing risks to population persistence. Climate change is expected to pose supplementary risks in this context of fragmented landscapes, and especially for river systems adaptation management programs are developed. The association of habitat quality and quantity with the landscape dynamics and resilience to human-induced disturbances is still poorly understood in the context of species survival and colonization processes, but essential to prioritize conservation and restoration actions. We present a modelling approach that elucidates network connectivity and landscape dynamics in spatial and temporal context to identify vital corridors and conservation priorities in the Loire river and its tributaries. Alteration of flooding and flow regimes is believed to be critical to population dynamics in river ecosystems. Still, little is known of critical levels of alteration both spatially and temporally. We applied metapopulation modelling approaches for a dispersal-limited tree species, white elm; and a recruitment-limited tree species, black poplar. In different model steps the connectivity and natural dynamics of the river landscape are confronted with physical alterations (dams/dykes) to species survival and then future scenarios for climatic changes and potential adaptation measures are entered in the model and translated in population persistence over the river basin. For the two tree species we highlighted crucial network zones in relation to habitat quality and connectivity. Where the human impact model already shows currently restricted metapopulation development, climate change is projected to aggravate this persistence perspective substantially. For both species a significant drawback to the basin population is observed, with 1/3 for elm and ¼ for poplar after 25 years already. But proposed adaptation measures prove effective to even

  4. Bridging the Timescales of Single-Cell and Population Dynamics

    Science.gov (United States)

    Jafarpour, Farshid; Wright, Charles S.; Gudjonson, Herman; Riebling, Jedidiah; Dawson, Emma; Lo, Klevin; Fiebig, Aretha; Crosson, Sean; Dinner, Aaron R.; Iyer-Biswas, Srividya

    2018-04-01

    How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a data-validated theoretical framework that accounts for observables at both single-cell and population scales. We derive exact analytical complete time-dependent solutions to cell-age distributions and population growth rates as functionals of the underlying interdivision time distributions, for symmetric and asymmetric cell division. These results provide insights into the surprising implications of stochastic single-cell dynamics for population growth. Using our results for asymmetric division, we deduce the time to transition from the reproductively quiescent (swarmer) to the replication-competent (stalked) stage of the Caulobacter crescentus life cycle. Remarkably, population numbers can spontaneously oscillate with time. We elucidate the physics leading to these population oscillations. For C. crescentus cells, we show that a simple measurement of the population growth rate, for a given growth condition, is sufficient to characterize the condition-specific cellular unit of time and, thus, yields the mean (single-cell) growth and division timescales, fluctuations in cell division times, the cell-age distribution, and the quiescence timescale.

  5. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-01-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

  6. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-05-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

  7. Crater Lake Apoyo Revisited - Population Genetics of an Emerging Species Flock

    Science.gov (United States)

    Geiger, Matthias F.; McCrary, Jeffrey K.; Schliewen, Ulrich K.

    2013-01-01

    The polytypic Nicaraguan Midas cichlids ( Amphilophus cf. citrinellus) have been established as a model system for studying the mechanisms of speciation and patterns of diversification in allopatry and sympatry. The species assemblage in Crater Lake Apoyo has been accepted as a textbook example for sympatric speciation. Here, we present a first comprehensive data set of population genetic (mtDNA & AFLPs) proxies of species level differentiation for a representative set of individuals of all six endemic Amphilophus species occurring in Crater Lake Apoyo. AFLP genetic differentiation was partitioned into a neutral and non-neutral component based on outlier-loci detection approaches, and patterns of species divergence were explored with Bayesian clustering methods. Substantial levels of admixture between species were detected, indicating different levels of reproductive isolation between the six species. Analysis of neutral genetic variation revealed several A . zaliosus as being introgressed by an unknown contributor, hereby rendering the sympatrically evolving L. Apoyo flock polyphyletic. This is contrasted by the mtDNA analysis delivering a clear monophyly signal with Crater Lake Apoyo private haplotypes characterising all six described species, but also demonstrating different demographic histories as inferred from pairwise mismatch distributions. PMID:24086393

  8. Solution of the spatial neutral model yields new bounds on the Amazonian species richness

    Science.gov (United States)

    Shem-Tov, Yahav; Danino, Matan; Shnerb, Nadav M.

    2017-02-01

    Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with spatial structure, but the analytic results presented so far are limited to well-mixed or mainland-island scenarios. Here we combine analytic results and numerics to obtain an approximate solution for the species abundance distribution and the species richness for the neutral model on continuous landscape. We show how the regional diversity increases when the recruitment length decreases and the spatial segregation of species grows. Our results are supported by extensive numerical simulations and allow one to probe the numerically inaccessible regime of large-scale systems with extremely small mutation/speciation rates. Model predictions are compared with the findings of recent large-scale surveys of tropical trees across the Amazon basin, yielding new bounds for the species richness (between 13100 and 15000) and the number of singleton species (between 455 and 690).

  9. Stochastic population and epidemic models persistence and extinction

    CERN Document Server

    Allen, Linda J S

    2015-01-01

    This monograph provides a summary of the basic theory of branching processes for single-type and multi-type processes. Classic examples of population and epidemic models illustrate the probability of population or epidemic extinction obtained from the theory of branching processes. The first chapter develops the branching process theory, while in the second chapter two applications to population and epidemic processes of single-type branching process theory are explored. The last two chapters present multi-type branching process applications to epidemic models, and then continuous-time and continuous-state branching processes with applications. In addition, several MATLAB programs for simulating stochastic sample paths  are provided in an Appendix. These notes originated as part of a lecture series on Stochastics in Biological Systems at the Mathematical Biosciences Institute in Ohio, USA. Professor Linda Allen is a Paul Whitfield Horn Professor of Mathematics in the Department of Mathematics and Statistics ...

  10. Integrating single-cell transcriptomic data across different conditions, technologies, and species.

    Science.gov (United States)

    Butler, Andrew; Hoffman, Paul; Smibert, Peter; Papalexi, Efthymia; Satija, Rahul

    2018-06-01

    Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

  11. Population dynamics of Pseudo-nitzschia species ...

    African Journals Online (AJOL)

    The genus Pseudo-nitzschia is a chain-forming diatom comprising about 30 species some of which are known to produce domoic acid (DA) that causes amnesic shellfish poisoning (ASP). The current study aimed at assessing the population dynamics of Pseudo-nitzschia in the near shore waters of Dar es Salaam. Samples ...

  12. Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago.

    Science.gov (United States)

    Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E; Pellissier, Loïc

    2018-03-01

    Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

  13. Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago

    Science.gov (United States)

    Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E.

    2018-01-01

    Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns. PMID:29657753

  14. Parameter Estimates in Differential Equation Models for Population Growth

    Science.gov (United States)

    Winkel, Brian J.

    2011-01-01

    We estimate the parameters present in several differential equation models of population growth, specifically logistic growth models and two-species competition models. We discuss student-evolved strategies and offer "Mathematica" code for a gradient search approach. We use historical (1930s) data from microbial studies of the Russian biologist,…

  15. Impacts of biogeographic history and marginal population genetics on species range limits: a case study of Liriodendron chinense.

    Science.gov (United States)

    Yang, Aihong; Dick, Christopher W; Yao, Xiaohong; Huang, Hongwen

    2016-05-10

    Species ranges are influenced by past climate oscillations, geographical constraints, and adaptive potential to colonize novel habitats at range limits. This study used Liriodendron chinense, an important temperate Asian tree species, as a model system to evaluate the roles of biogeographic history and marginal population genetics in determining range limits. We examined the demographic history and genetic diversity of 29 L. chinense populations using both chloroplast and nuclear microsatellite loci. Significant phylogeographic structure was recovered with haplotype clusters coinciding with major mountain regions. Long-term demographical stability was suggested by mismatch distribution analyses, neutrality tests, and ecological niche models (ENM) and suggested the existence of LGM refuges within mountain regions. Differences in genetic diversity between central and marginal populations were not significant for either genomic region. However, asymmetrical gene flow was inferred from central populations to marginal populations, which could potentially limit range adaptation and expansion of L. chinense.

  16. The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations.

    Science.gov (United States)

    Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

    2017-01-01

    Wild tomatoes are a valuable source of disease resistance germplasm for tomato ( Solanum lycopersicum ) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense , both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense . We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens ( Alternaria solani , Phytophthora infestans and a Fusarium sp .) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense , resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

  17. Stochastic adaptation and fold-change detection: from single-cell to population behavior

    Directory of Open Access Journals (Sweden)

    Leier André

    2011-02-01

    Full Text Available Abstract Background In cell signaling terminology, adaptation refers to a system's capability of returning to its equilibrium upon a transient response. To achieve this, a network has to be both sensitive and precise. Namely, the system must display a significant output response upon stimulation, and later on return to pre-stimulation levels. If the system settles at the exact same equilibrium, adaptation is said to be 'perfect'. Examples of adaptation mechanisms include temperature regulation, calcium regulation and bacterial chemotaxis. Results We present models of the simplest adaptation architecture, a two-state protein system, in a stochastic setting. Furthermore, we consider differences between individual and collective adaptive behavior, and show how our system displays fold-change detection properties. Our analysis and simulations highlight why adaptation needs to be understood in terms of probability, and not in strict numbers of molecules. Most importantly, selection of appropriate parameters in this simple linear setting may yield populations of cells displaying adaptation, while single cells do not. Conclusions Single cell behavior cannot be inferred from population measurements and, sometimes, collective behavior cannot be determined from the individuals. By consequence, adaptation can many times be considered a purely emergent property of the collective system. This is a clear example where biological ergodicity cannot be assumed, just as is also the case when cell replication rates are not homogeneous, or depend on the cell state. Our analysis shows, for the first time, how ergodicity cannot be taken for granted in simple linear examples either. The latter holds even when cells are considered isolated and devoid of replication capabilities (cell-cycle arrested. We also show how a simple linear adaptation scheme displays fold-change detection properties, and how rupture of ergodicity prevails in scenarios where transitions between

  18. Optimizing conservation of migratory species over their full annual cycle in the Western Hemisphere

    OpenAIRE

    Bennett, Joseph; Auer, Tom; Fink, Daniel; Arcese, Peter; Rodewald, Amanda; Wilson, Scott; Schuster, Richard

    2018-01-01

    Strategic plans to conserve migratory species require detailed knowledge on species distribution, abundance, and habitat use over the annual cycle, but such data are lacking for most species. We developed a hemispheric approach to planning using spatiotemporally explicit species abundance models to prioritize land needed to conserve ≥17% of the global populations of 109 species of Neotropical migratory birds. The efficiency of annual cycle plans was evaluated in comparisons to single-season p...

  19. The roles of competition and habitat in the dynamics of populations and species distributions.

    Science.gov (United States)

    Yackulic, Charles B; Reid, Janice; Nichols, James D; Hines, James E; Davis, Raymond; Forsman, Eric

    2014-02-01

    The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl, Strix varia) and a resident species (Northern Spotted Owl, Strix occidentalis caurina) in a 1000-km study area over a 22-year period. Past studies of these competitors have focused on the dynamics of one species at a time, hindering efforts to parse out the roles of habitat and competition and to forecast the future of the resident species. In addition, while these studies accounted for the imperfect detection of the focal species, no multi-season analysis of these species has accounted for the imperfect detection of the secondary species, potentially biasing inference. We analyzed survey data using models that combine the general multistate-multi-season occupancy modeling framework with autologistic modeling, allowing us to account for important aspects of our study system. We found that local extinction probability increases for each species when the other is present; however, the effect of the invader on the resident is greater. Although the species prefer different habitats, these habitats are highly correlated at the patch scale, and the impacts of invader on the resident are greatest in patches that would otherwise be optimal. As a consequence, competition leads to a weaker relationship between habitat and Northern Spotted Owl occupancy. Colonization and extinction rates of the invader are closely related to neighborhood occupancy, and over the first half of the study the availability of colonists limited the rate of population growth. Competition is likely to exclude the resident species, both through its immediate effects on local extinction and by indirectly lowering colonization rates as

  20. The geography of demography: long-term demographic studies and species distribution models reveal a species border limited by adaptation.

    Science.gov (United States)

    Eckhart, V M; Geber, M A; Morris, W F; Fabio, E S; Tiffin, P; Moeller, D A

    2011-10-01

    Potential causes of species' geographic distribution limits fall into two broad classes: (1) limited adaptation across spatially variable environments and (2) limited opportunities to colonize unoccupied areas. Combining demographic studies, analyses of demographic responses to environmental variation, and species distribution models, we investigated the causes of range limits in a model system, the eastern border of the California annual plant Clarkia xantiana ssp. xantiana. Vital rates of 20 populations varied with growing season temperature and precipitation: fruit number and overwinter survival of 1-year-old seeds declined steeply, while current-year seed germination increased modestly along west-to-east gradients in decreasing temperature, decreasing mean precipitation, and increasing variation in precipitation. Long-term stochastic finite rate of increase, λ(s), exhibited a fourfold range and varied among geologic surface materials as well as with temperature and precipitation. Growth rate declined significantly toward the eastern border, falling below 1 in three of the five easternmost populations. Distribution models employing demographically important environmental variables predicted low habitat favorability beyond the eastern border. Models that filtered or weighted population presences by λ(s) predicted steeper eastward declines in favorability and assigned greater roles in setting the distribution to among-year variation in precipitation and to geologic surface material. These analyses reveal a species border likely set by limited adaptation to declining environmental quality.

  1. Analysis of single hyphal growth and fragmentation in submerged cultures using a population model

    DEFF Research Database (Denmark)

    Krabben, Preben; Nielsen, Søren; Michelsen, Michael Locht

    1997-01-01

    Descriptions of population dynamics in submerged cultures are important when studying the mechanisms of growth and fragmentation of filamentous microorganisms. Population models are traditionally formulated as population balance equations. Population models of filamentous morphology are difficult...... to solve because of random fragmentation, which introduces an integral term into the population balance equations. Balances for the systemic properties, e.g. concentration of hyphal elements, substrate concentration, average total hyphal length, and average number of growing tips, are set up. Based...... on these balances one can solve the inverse problem, i.e. determination of kinetic parameters directly from measurements of the hyphal morphology. Both a Monte Carlo method and a discretization method have been used to calculate the steady-state population distribution. The two methods are compared and the Monte...

  2. A Single Transcriptome of a Green Toad (Bufo viridis Yields Candidate Genes for Sex Determination and -Differentiation and Non-Anonymous Population Genetic Markers.

    Directory of Open Access Journals (Sweden)

    Jörn F Gerchen

    Full Text Available Large genome size, including immense repetitive and non-coding fractions, still present challenges for capacity, bioinformatics and thus affordability of whole genome sequencing in most amphibians. Here, we test the performance of a single transcriptome to understand whether it can provide a cost-efficient resource for species with large unknown genomes. Using RNA from six different tissues from a single Palearctic green toad (Bufo viridis specimen and Hiseq2000, we obtained 22,5 Mio reads and publish >100,000 unigene sequences. To evaluate efficacy and quality, we first use this data to identify green toad specific candidate genes, known from other vertebrates for their role in sex determination and differentiation. Of a list of 37 genes, the transcriptome yielded 32 (87%, many of which providing the first such data for this non-model anuran species. However, for many of these genes, only fragments could be retrieved. In order to allow also applications to population genetics, we further used the transcriptome for the targeted development of 21 non-anonymous microsatellites and tested them in genetic families and backcrosses. Eleven markers were specifically developed to be located on the B. viridis sex chromosomes; for eight markers we can indeed demonstrate sex-specific transmission in genetic families. Depending on phylogenetic distance, several markers, which are sex-linked in green toads, show high cross-amplification success across the anuran phylogeny, involving nine systematic anuran families. Our data support the view that single transcriptome sequencing (based on multiple tissues provides a reliable genomic resource and cost-efficient method for non-model amphibian species with large genome size and, despite limitations, should be considered as long as genome sequencing remains unaffordable for most species.

  3. Extension of landscape-based population viability models to ecoregional scales for conservation planning

    Science.gov (United States)

    Thomas W. Bonnot; Frank R. III Thompson; Joshua Millspaugh

    2011-01-01

    Landscape-based population models are potentially valuable tools in facilitating conservation planning and actions at large scales. However, such models have rarely been applied at ecoregional scales. We extended landscape-based population models to ecoregional scales for three species of concern in the Central Hardwoods Bird Conservation Region and compared model...

  4. Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae occurring sympatrically in the Red River region of China

    Directory of Open Access Journals (Sweden)

    Liu eJian

    2015-09-01

    Full Text Available Delimitating species boundaries could be of critical importance when evaluating the species’ evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH and trnL-rps4 and two single copy nuclear (RPB1 and SmHP DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into Yuanjiang-Nanhun basin and Ejia-Jiepai basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the

  5. Population sensitivities of animals to chronic ionizing radiation-model predictions from mice to elephant.

    Science.gov (United States)

    Sazykina, Tatiana G

    2018-02-01

    Model predictions of population response to chronic ionizing radiation (endpoint 'morbidity') were made for 11 species of warm-blooded animals, differing in body mass and lifespan - from mice to elephant. Predictions were made also for 3 bird species (duck, pigeon, and house sparrow). Calculations were based on analytical solutions of the mathematical model, simulating a population response to low-LET ionizing radiation in an ecosystem with a limiting resource (Sazykina, Kryshev, 2016). Model parameters for different species were taken from biological and radioecological databases; allometric relationships were employed for estimating some parameter values. As a threshold of decreased health status in exposed populations ('health threshold'), a 10% reduction in self-repairing capacity of organisms was suggested, associated with a decline in ability to sustain environmental stresses. Results of the modeling demonstrate a general increase of population vulnerability to ionizing radiation in animal species of larger size and longevity. Populations of small widespread species (mice, house sparrow; body mass 20-50 g), which are characterized by intensive metabolism and short lifespan, have calculated 'health thresholds' at dose rates about 6.5-7.5 mGy day -1 . Widespread animals with body mass 200-500 g (rat, common pigeon) - demonstrate 'health threshold' values at 4-5 mGy day -1 . For populations of animals with body mass 2-5 kg (rabbit, fox, raccoon), the indicators of 10% health decrease are in the range 2-3.4 mGy day -1 . For animals with body mass 40-100 kg (wolf, sheep, wild boar), thresholds are within 0.5-0.8 mGy day -1 ; for herbivorous animals with body mass 200-300 kg (deer, horse) - 0.5-0.6 mGy day -1 . The lowest health threshold was estimated for elephant (body mass around 5000 kg) - 0.1 mGy day -1 . According to the model results, the differences in population sensitivities of warm-blooded animal species to ionizing radiation are generally

  6. Balancing energy development and conservation: A method utilizing species distribution models

    Science.gov (United States)

    Jarnevich, C.S.; Laubhan, M.K.

    2011-01-01

    Alternative energy development is increasing, potentially leading to negative impacts on wildlife populations already stressed by other factors. Resource managers require a scientifically based methodology to balance energy development and species conservation, so we investigated modeling habitat suitability using Maximum Entropy to develop maps that could be used with other information to help site energy developments. We selected one species of concern, the Lesser Prairie-Chicken (LPCH; Tympanuchus pallidicinctus) found on the southern Great Plains of North America, as our case study. LPCH populations have been declining and are potentially further impacted by energy development. We used LPCH lek locations in the state of Kansas along with several environmental and anthropogenic parameters to develop models that predict the probability of lek occurrence across the landscape. The models all performed well as indicated by the high test area under the curve (AUC) scores (all >0.9). The inclusion of anthropogenic parameters in models resulted in slightly better performance based on AUC values, indicating that anthropogenic features may impact LPCH lek habitat suitability. Given the positive model results, this methodology may provide additional guidance in designing future survey protocols, as well as siting of energy development in areas of marginal or unsuitable habitat for species of concern. This technique could help to standardize and quantify the impacts various developments have upon at-risk species. ?? 2011 Springer Science+Business Media, LLC (outside the USA).

  7. The roles of competition and habitat in the dynamics of populations and species distributions

    Science.gov (United States)

    Yackulic, Charles Brandon; Reid, Janice; Nichols, James D.; Hines, James E.; Davis, Raymond; Forsman, Eric

    2014-01-01

    The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading (barred owl: Strix varia) and a resident species (Northern spotted owl: Strix occidentalis caurina) in a 1000 km2 study area over a 22 - year period. Past studies of these competitors have focused on the dynamics of one species at a time, hindering efforts to parse out the roles of habitat and competition and to forecast the future of the resident species. In addition, while these studies accounted for the imperfect detection of the focal species, no multiseason analysis of these species has accounted for the imperfect detection of the secondary species, potentially biasing inference. We analyze survey data using models that combine the general multistate-multiseason occupancy modeling framework with autologistic modeling - allowing us to account for important aspects of our study system. We find that local extinction probability increases for each species when the other is present; however, the effect of the invader on the resident is greater. Although the species prefer different habitats, these habitats are highly correlated at the patch scale and the impacts of invader on the resident are greatest in patches that would otherwise be optimal. As a consequence, competition leads to a weaker relationship between habitat and Northern spotted owl occupancy. Colonization and extinction rates of the invader are closely related to neighborhood occupancy, and over the first half of the study the availability of colonists limited the rate of population growth. Competition is likely to exclude the resident species both through its immediate effects on local extinction, and by indirectly lowering colonization rates as Northern

  8. Molecular markers reveal limited population genetic structure in a North American corvid, Clark's nutcracker (Nucifraga columbiana.

    Directory of Open Access Journals (Sweden)

    Kimberly M Dohms

    Full Text Available The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark's nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker's encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark's nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark's nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark's nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges do not appear to restrict gene flow in Clark's nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets.

  9. Modelling the propagation of effects of chronic exposure to ionising radiation from individuals to populations

    Energy Technology Data Exchange (ETDEWEB)

    Alonzo, F. [Laboratory of Environmental Modelling, DEI/SECRE/LME, Institute of Radioprotection and Nuclear Safety (IRSN), Cadarache, Building 159, BP3, 13115 St-Paul-lez-Durance Cedex (France); Laboratory of Radioecology and Ecotoxicology, DEI/SECRE/LRE, Institute of Radioprotection and Nuclear Safety (IRSN), Cadarache Building 186, BP3, 13115 St-Paul-lez-Durance Cedex (France)], E-mail: frederic.alonzo@irsn.fr; Hertel-Aas, T. [Department of Plant and Environmental Sciences, P.O. Box 5003, Norwegian University of Life Sciences, 1432 Aas (Norway); Gilek, M. [School of Life Sciences, Soedertoern University College, 14189 Huddinge (Sweden); Gilbin, R. [Laboratory of Radioecology and Ecotoxicology, DEI/SECRE/LRE, Institute of Radioprotection and Nuclear Safety (IRSN), Cadarache Building 186, BP3, 13115 St-Paul-lez-Durance Cedex (France); Oughton, D.H. [Department of Plant and Environmental Sciences, P.O. Box 5003, Norwegian University of Life Sciences, 1432 Aas (Norway); Garnier-Laplace, J. [Laboratory of Radioecology and Ecotoxicology, DEI/SECRE/LRE, Institute of Radioprotection and Nuclear Safety (IRSN), Cadarache Building 186, BP3, 13115 St-Paul-lez-Durance Cedex (France)

    2008-09-15

    This study evaluated the potential effect of ionising radiation on population growth using simple population models and parameter values derived from chronic exposure experiments in two invertebrate species with contrasting life-history strategies. In the earthworm Eisenia fetida, models predicted increasing delay in population growth with increasing gamma dose rate (up to 0.6 generation times at 11 mGy h{sup -1}). Population extinction was predicted at 43 mGy h{sup -1}. In the microcrustacean Daphnia magna, models predicted increasing delay in population growth with increasing alpha dose rate (up to 0.8 generation times at 15.0 mGy h{sup -1}), only after two successive generations were exposed. The study examined population effects of changes in different individual endpoints (including survival, number of offspring produced and time to first reproduction). Models showed that the two species did not respond equally to equivalent levels of change, the fast growing daphnids being more susceptible to reduction in fecundity or delay in reproduction than the slow growing earthworms. This suggested that susceptibility of a population to ionising radiation cannot be considered independent of the species' life history.

  10. The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations

    Directory of Open Access Journals (Sweden)

    Remco Stam

    2017-01-01

    Full Text Available Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp. and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

  11. The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations

    Science.gov (United States)

    Scheikl, Daniela; Tellier, Aurélien

    2017-01-01

    Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved. PMID:28133579

  12. Effects of sediment-spiked lufenuron on benthic macroinvertebrates in outdoor microcosms and single-species toxicity tests

    Energy Technology Data Exchange (ETDEWEB)

    Brock, T.C.M., E-mail: theo.brock@wur.nl [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands); Bas, D.A. [Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam (Netherlands); Belgers, J.D.M. [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands); Bibbe, L. [Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam (Netherlands); Boerwinkel, M-C.; Crum, S.J.H. [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands); Diepens, N.J. [Department of Aquatic Ecology and Water Quality Management, Wageningen University, P.O. Box 47, 6700 AA Wageningen (Netherlands); Kraak, M.H.S.; Vonk, J.A. [Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam (Netherlands); Roessink, I. [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands)

    2016-08-15

    Highlights: • In outdoor microcosms constructed with lufenuron-spiked sediment we observed that this insecticide persistent in the sediment compartment. • Sediment exposure to lufenuron caused population-level declines (insects and crustaceans) and increases (mainly oligochaete worms) of benthic invertebrates. • The direct and indirect effects observed in the microcosms were supported by results of sediment-spiked single species tests with Chironomus riparius, Hyalella azteca and Lumbriculus variegatus. • The tier-1 effect assessment procedure for sediment organisms recommended by the European Food Safety Authority is protective for the treatment-related responses observed in the microcosm test. - Abstract: Sediment ecotoxicity studies were conducted with lufenuron to (i) complement the results of a water-spiked mesocosm experiment with this lipophilic benzoylurea insecticide, (ii) to explore the predictive value of laboratory single-species tests for population and community-level responses of benthic macroinvertebrates, and (iii) to calibrate the tier-1 effect assessment procedure for sediment organisms. For this purpose the concentration-response relationships for macroinvertebrates between sediment-spiked microcosms and those of 28-d sediment-spiked single-species toxicity tests with Chironomus riparius, Hyalella azteca and Lumbriculus variegatus were compared. Lufenuron persisted in the sediment of the microcosms. On average, 87.7% of the initial lufenuron concentration could still be detected in the sediment after 12 weeks. Overall, benthic insects and crustaceans showed treatment-related declines and oligochaetes treatment-related increases. The lowest population-level NOEC in the microcosms was 0.79 μg lufenuron/g organic carbon in dry sediment (μg a.s./g OC) for Tanytarsini, Chironomini and Dero sp. Multivariate analysis of the responses of benthic macroinvertebrates revealed a community-level NOEC of 0.79 μg a.s./g OC. The treatment

  13. Species conservation and natural variation among populations [Chapter 5

    Science.gov (United States)

    Leonard F. Ruggiero; Michael K. Schwartz; Keith B. Aubry; Charles J. Krebs; Amanda Stanley; Steven W. Buskirk

    2000-01-01

    In conservation planning, the importance of natural variation is often given inadequate consideration. However, ignoring the implications of variation within species may result in conservation strategies that jeopardize, rather than conserve, target species (see Grieg 1979; Turcek 1951; Storfer 1999). Natural variation in the traits of individuals and populations is...

  14. Linking population viability, habitat suitability, and landscape simulation models for conservation planning

    Science.gov (United States)

    Michael A. Larson; Frank R., III Thompson; Joshua J. Millspaugh; William D. Dijak; Stephen R. Shifley

    2004-01-01

    Methods for habitat modeling based on landscape simulations and population viability modeling based on habitat quality are well developed, but no published study of which we are aware has effectively joined them in a single, comprehensive analysis. We demonstrate the application of a population viability model for ovenbirds (Seiurus aurocapillus)...

  15. Predicting weed problems in maize cropping by species distribution modelling

    Directory of Open Access Journals (Sweden)

    Bürger, Jana

    2014-02-01

    Full Text Available Increasing maize cultivation and changed cropping practices promote the selection of typical maize weeds that may also profit strongly from climate change. Predicting potential weed problems is of high interest for plant production. Within the project KLIFF, experiments were combined with species distribution modelling for this task in the region of Lower Saxony, Germany. For our study, we modelled ecological and damage niches of nine weed species that are significant and wide spread in maize cropping in a number of European countries. Species distribution models describe the ecological niche of a species, these are the environmental conditions under which a species can maintain a vital population. It is also possible to estimate a damage niche, i.e. the conditions under which a species causes damage in agricultural crops. For this, we combined occurrence data of European national data bases with high resolution climate, soil and land use data. Models were also projected to simulated climate conditions for the time horizon 2070 - 2100 in order to estimate climate change effects. Modelling results indicate favourable conditions for typical maize weed occurrence virtually all over the study region, but only a few species are important in maize cropping. This is in good accordance with the findings of an earlier maize weed monitoring. Reaction to changing climate conditions is species-specific, for some species neutral (E. crus-galli, other species may gain (Polygonum persicaria or loose (Viola arvensis large areas of suitable habitats. All species with damage potential under present conditions will remain important in maize cropping, some more species will gain regional importance (Calystegia sepium, Setara viridis.

  16. DEFINING RECOVERY GOALS AND STRATEGIES FOR ENDANGERED SPECIES USING SPATIALLY-EXPLICIT POPULATION MODELS

    Science.gov (United States)

    We used a spatially explicit population model of wolves (Canis lupus) to propose a framework for defining rangewide recovery priorities and finer-scale strategies for regional reintroductions. The model predicts that Yellowstone and central Idaho, where wolves have recently been ...

  17. Emergence of target waves in paced populations of cyclically competing species

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Luoluo; Zhou Tao; Wang Binghong [Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Perc, Matjaz [Department of Physics, Faculty of Natural Sciences and Mathematics, University of Maribor, Koroska cesta 160, SI-2000 Maribor (Slovenia); Huang Xin [Department of Physics, University of Science and Technology of China, Hefei 230026 (China)], E-mail: jiangluo@mail.ustc.edu.cn, E-mail: zhutou@ustc.edu, E-mail: matjaz.perc@uni-mb.si, E-mail: bhwang@ustc.edu.cn

    2009-10-15

    We investigate the emergence of target waves in a cyclic predator-prey model incorporating a periodic current of the three competing species in a small area situated at the center of a square lattice. The periodic current acts as a pacemaker, trying to impose its rhythm on the overall spatiotemporal evolution of the three species. We show that the pacemaker is able to nucleate target waves that eventually spread across the whole population, whereby three routes leading to this phenomenon can be distinguished depending on the mobility of the three species and the oscillation period of the localized current. First, target waves can emerge due to the synchronization between the periodic current and oscillations of the density of the three species on the spatial grid. The second route is similar to the first, the difference being that the synchronization sets in only intermittently. Finally, the third route toward target waves is realized when the frequency of the pacemaker is much higher than that characterizing the oscillations of the overall density of the three species. By considering the mobility and frequency of the current as variable parameters, we thus provide insights into the mechanisms of pattern formation resulting from the interplay between local and global dynamics in systems governed by cyclically competing species.

  18. Malaria in Africa: vector species' niche models and relative risk maps.

    Directory of Open Access Journals (Sweden)

    Alexander Moffett

    2007-09-01

    Full Text Available A central theoretical goal of epidemiology is the construction of spatial models of disease prevalence and risk, including maps for the potential spread of infectious disease. We provide three continent-wide maps representing the relative risk of malaria in Africa based on ecological niche models of vector species and risk analysis at a spatial resolution of 1 arc-minute (9 185 275 cells of approximately 4 sq km. Using a maximum entropy method we construct niche models for 10 malaria vector species based on species occurrence records since 1980, 19 climatic variables, altitude, and land cover data (in 14 classes. For seven vectors (Anopheles coustani, A. funestus, A. melas, A. merus, A. moucheti, A. nili, and A. paludis these are the first published niche models. We predict that Central Africa has poor habitat for both A. arabiensis and A. gambiae, and that A. quadriannulatus and A. arabiensis have restricted habitats in Southern Africa as claimed by field experts in criticism of previous models. The results of the niche models are incorporated into three relative risk models which assume different ecological interactions between vector species. The "additive" model assumes no interaction; the "minimax" model assumes maximum relative risk due to any vector in a cell; and the "competitive exclusion" model assumes the relative risk that arises from the most suitable vector for a cell. All models include variable anthrophilicity of vectors and spatial variation in human population density. Relative risk maps are produced from these models. All models predict that human population density is the critical factor determining malaria risk. Our method of constructing relative risk maps is equally general. We discuss the limits of the relative risk maps reported here, and the additional data that are required for their improvement. The protocol developed here can be used for any other vector-borne disease.

  19. Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes.

    Science.gov (United States)

    Vendrami, David L J; Shah, Abhijeet; Telesca, Luca; Hoffman, Joseph I

    2016-06-01

    Transcriptional profiling not only provides insights into patterns of gene expression, but also generates sequences that can be mined for molecular markers, which in turn can be used for population genetic studies. As part of a large-scale effort to better understand how commercially important European shellfish species may respond to ocean acidification, we therefore mined the transcriptomes of four species (the Pacific oyster Crassostrea gigas, the blue mussel Mytilus edulis, the great scallop Pecten maximus and the blunt gaper Mya truncata) for single nucleotide polymorphisms (SNPs). Illumina data for C. gigas, M. edulis and P. maximus and 454 data for M. truncata were interrogated using GATK and SWAP454 respectively to identify between 8267 and 47,159 high quality SNPs per species (total=121,053 SNPs residing within 34,716 different contigs). We then annotated the transcripts containing SNPs to reveal homology to diverse genes. Finally, as oceanic pH affects the ability of organisms to incorporate calcium carbonate, we honed in on genes implicated in the biomineralization process to identify a total of 1899 SNPs in 157 genes. These provide good candidates for biomarkers with which to study patterns of selection in natural or experimental populations. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. The epidemiology of Candida species associated with vulvovaginal candidiasis in an Iranian patient population.

    Science.gov (United States)

    Mahmoudi Rad, M; Zafarghandi, S; Abbasabadi, B; Tavallaee, M

    2011-04-01

    Vulvovaginal candidiasis is a common infection among women worldwide. According to previous epidemiological studies, Candida albicans is the most common species of Candida. The prevalence of non-Candida species, however, is increasing. Identification of Candida species among the population will not only help health professionals to choose suitable antifungal treatments, but also prevent development of drug resistance. The aim of this study was to identify, using chromogenic agar medium, the Candida species associated with vulvovaginal candidiasis among a sample of the Iranian population. In a prospective cohort study during a two year period from March 2006 to March 2008, swab samples of vaginal discharge/secretion were taken from 200 patients admitted to the gynecology clinic of Mahdieh Hospital (Tehran, Iran) with a clinical presentation suggestive of vulvovaginal candidiasis. The isolates obtained were cultured on Sabouraud dextrose agar and chromogenic agar medium. Candida species were also identified by germ tube formation in serum, chlamydospore production on Corn Meal Agar and carbohydrate absorption using the API 20C-AUX kit. Participants were asked to complete a questionnaire investigating the risk factors associated with candidiasis. An assessment of the different species of recurrent and non-recurrent candidiasis was also made. Descriptive statistics, chi-square test, and t-test were used to analyze the data. A total of 191 isolates were obtained from 175 vaginal specimens. Candida albicans accounted for 67% of the strains including single and mixed infections. The other identified species were Candida glabrata (18.3%), Candida tropicalis (6.8%), Candida krusei (5.8%), Candida parapsilosis (1.6%), and Candida guilliermondii (0.5%) respectively. Mixed infection with two or more species of Candida was seen in 10.3% of patients. The most common mixed cause was the combination of Candida albicans and Candida glabrata. Participants who were sexually active

  1. Ecological niche modelling and nDNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding.

    Science.gov (United States)

    Hawlitschek, Oliver; Porch, Nick; Hendrich, Lars; Balke, Michael

    2011-02-09

    DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data. The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n. In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species.

  2. Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity.

    Science.gov (United States)

    Karimi, G; Jamaluddin, R; Mohtarrudin, N; Ahmad, Z; Khazaai, H; Parvaneh, M

    2017-10-01

    Recent studies have reported beneficial effects of specific probiotics on obesity. However, the difference in the anti-obesity effects of probiotics as single species and dual species is still uncertain. Therefore, we aimed to compare the efficacy of single and dual species of bacteria on markers of obesity in high-fat diet-induced obese rats. A total of 40 male Sprague-Dawley rats were assigned to one of five groups of varying diets as follows: standard diet, high fat diet (HFD), HFD supplemented with Lactobacillus casei strain Shirota, HFD supplemented with Bifidobacterium longum and HFD supplemented with a mixture of these two bacterial species. After 15 weeks of supplementation, the animals were examined for changes in body weight, body fat, total count of bacteria in fecal, blood serum lipid profile, leptin, adiponectin and inflammatory biomarkers. Histological analysis of the liver and adipose tissue was performed and the hepatic mRNA expression levels of genes related to lipid metabolism were measured. It was found that probiotic supplementation of either B. longum or a mixture of B. longum and LcS bacteria significantly reduced weight and triglycerides in the HFD groups. Supplementation of B. longum bacteria showed better results in terms of modulating leptin level, fat mass, adipocyte size and lipoprotein lipase expression, as well as increasing adiponectin and peroxisome proliferator-activated receptors-γ expression compared to dual species of bacteria. No significant differences were observed in the total count of fecal bacteria, glucose and inflammatory biomarker levels between supplemented groups. B. longum supplementation in obesity was more beneficial in metabolic profile changes than the mixture species. Copyright © 2017 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B

  3. Speciation in the Derrida-Higgs model with finite genomes and spatial populations

    Science.gov (United States)

    de Aguiar, Marcus A. M.

    2017-02-01

    The speciation model proposed by Derrida and Higgs demonstrated that a sexually reproducing population can split into different species in the absence of natural selection or any type of geographic isolation, provided that mating is assortative and the number of genes involved in the process is infinite. Here we revisit this model and simulate it for finite genomes, focusing on the question of how many genes it actually takes to trigger neutral sympatric speciation. We find that, for typical parameters used in the original model, it takes the order of 105 genes. We compare the results with a similar spatially explicit model where about 100 genes suffice for speciation. We show that when the number of genes is small the species that emerge are strongly segregated in space. For a larger number of genes, on the other hand, the spatial structure of the population is less important and the species distribution overlap considerably.

  4. Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago.

    Science.gov (United States)

    Legrand, Delphine; Vautrin, Dominique; Lachaise, Daniel; Cariou, Marie-Louise

    2011-07-01

    Drosophila sechellia is closely related to the cosmopolitan and widespread model species, D. simulans. This species, endemic to the Seychelles archipelago, is specialized on the fruits of Morinda citrifolia, and harbours the lowest overall genetic diversity compared to other species of Drosophila. This low diversity is associated with a small population size. In addition, no obvious population structure has been evidenced so far across islands of the Seychelles archipelago. Here, a microsatellite panel of 17 loci in ten populations from nine islands of the Seychelles was used to assess the effect of the D. sechellia's fragmented distribution on the fine-scale population genetic structure, the migration pattern, as well as on the demography of the species. Contrary to previous results, also based on microsatellites, no evidence for population contraction in D. sechellia was found. The results confirm previous studies based on gene sequence polymorphism that showed a long-term stable population size for this species. Interestingly, a pattern of Isolation By Distance which had not been described yet in D. sechellia was found, with evidence of first-generation migrants between some neighbouring islands. Bayesian structuring algorithm results were consistent with a split of D. sechellia into two main groups of populations: Silhouette/Mahé versus all the other islands. Thus, microsatellites suggest that variability in D. sechellia is most likely explained by local genetic exchanges between neighbouring islands that have recently resulted in slight differentiation of the two largest island populations from all the others.

  5. Physiological differentiation within a single-species biofilm fueled by serpentinization.

    Science.gov (United States)

    Brazelton, William J; Mehta, Mausmi P; Kelley, Deborah S; Baross, John A

    2011-01-01

    Carbonate chimneys at the Lost City hydrothermal field are coated in biofilms dominated by a single phylotype of archaea known as Lost City Methanosarcinales. In this study, we have detected surprising physiological complexity in single-species biofilms, which is typically indicative of multispecies biofilm communities. Multiple cell morphologies were visible within the biofilms by transmission electron microscopy, and some cells contained intracellular membranes that may facilitate methane oxidation. Both methane production and oxidation were detected at 70 to 80°C and pH 9 to 10 in samples containing the single-species biofilms. Both processes were stimulated by the presence of hydrogen (H(2)), indicating that methane production and oxidation are part of a syntrophic interaction. Metagenomic data included a sequence encoding AMP-forming acetyl coenzyme A synthetase, indicating that acetate may play a role in the methane-cycling syntrophy. A wide range of nitrogen fixation genes were also identified, many of which were likely acquired via lateral gene transfer (LGT). Our results indicate that cells within these single-species biofilms may have differentiated into multiple physiological roles to form multicellular communities linked by metabolic interactions and LGT. Communities similar to these Lost City biofilms are likely to have existed early in the evolution of life, and we discuss how the multicellular characteristics of ancient hydrogen-fueled biofilm communities could have stimulated ecological diversification, as well as unity of biochemistry, during the earliest stages of cellular evolution. Our previous work at the Lost City hydrothermal field has shown that its carbonate chimneys host microbial biofilms dominated by a single uncultivated "species" of archaea. In this paper, we integrate evidence from these previous studies with new data on the metabolic activity and cellular morphology of these archaeal biofilms. We conclude that the archaeal biofilm

  6. A method to assess the population-level consequences of wind energy facilities on bird and bat species: Chapter

    Science.gov (United States)

    Diffendorfer, James E.; Beston, Julie A.; Merrill, Matthew; Stanton, Jessica C.; Corum, Margo D.; Loss, Scott R.; Thogmartin, Wayne E.; Johnson, Douglas H.; Erickson, Richard A.; Heist, Kevin W.

    2016-01-01

    For this study, a methodology was developed for assessing impacts of wind energy generation on populations of birds and bats at regional to national scales. The approach combines existing methods in applied ecology for prioritizing species in terms of their potential risk from wind energy facilities and estimating impacts of fatalities on population status and trend caused by collisions with wind energy infrastructure. Methods include a qualitative prioritization approach, demographic models, and potential biological removal. The approach can be used to prioritize species in need of more thorough study as well as to identify species with minimal risk. However, the components of this methodology require simplifying assumptions and the data required may be unavailable or of poor quality for some species. These issues should be carefully considered before using the methodology. The approach will increase in value as more data become available and will broaden the understanding of anthropogenic sources of mortality on bird and bat populations.

  7. [Urbanization mechanisms in bird species: population systems transformations or adaptations at the individual level?].

    Science.gov (United States)

    Fridman, V S; Eremkin, G S; Zakharova-Kubareva, N Iu

    2008-01-01

    The present research deals with urbanization of wild bird and mammal species. Forms and mechanisms of population steadiness in the urban landscape have been examined. The urbanization process turned out to be a directed change of the population system forming de novo in the urbolandscape leading to a sustainable organization peculiar for the particular environment. The population organization of different types in urbolandscape is found to provide its stability under conditions of directed and fast changes accompanied with instability and heterogenous structure of habitats. It is shown that the same type of population organization meets the corresponding demands among different species settling in the urban environment. Its features are "openness" and "flowage" of the groups, far order of settlement levels and other units of population system, constant movements of the individuals between the groups as a respond to the signals of urboenvironment significant changes. The "urban" variant of the population system organization turns out to be opposite to that of the same species in the non-urban habitats. After formation of the urban types by the species and successful developing of the town, the urban population becomes separated from the maternal local population and begins to exist independently in the urban landscape. The variety of adaptation aberrations in ecology, behavior, and mode of life of urban birds is the population system stability function in the urban landscape and is not a results of individual selection. It is shown that the urbanization process of the species goes firstly on the population level being the system structure transformation developed by the species towards the most stable state in the town (city) territory. Only after the appearance of stable urban population, the urban individuals show the rapid growth of different changes in ecology, behavior, mode of life that was traditionally described by naturalists as species adaptation to the

  8. Incorporating parametric uncertainty into population viability analysis models

    Science.gov (United States)

    McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.

    2011-01-01

    Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.

  9. Fluctuations in a coupled population model

    International Nuclear Information System (INIS)

    Jakeman, E; Hopcraft, K I; Matthews, J O

    2005-01-01

    We investigate a discrete Markov process in which the immigration of individuals into one population is controlled by the fluctuations in another. We examine the effect of coupling back the second population to the first through a similar mechanism and derive exact solutions for the generating functions of the population statistics. We show that a stationary state exists over a certain parameter range and obtain expressions for moments and correlation functions in this regime. When more than two populations are coupled, cyclically transient oscillations and periodic behaviour of correlation functions are predicted. We demonstrate that if the initial distribution of either population is stable, or more generally has a power-law tail that falls off like N -(1+α) (0 < α < 1), then for certain parameter values there exists a stationary state that is also power law but not stable. This stationary state cannot be accessed from a single multiple immigrant population model, but arises solely from the nonlinear interaction of the coupled system

  10. Conservation of avian diversity in the Sierra Nevada: moving beyond a single-species management focus.

    Directory of Open Access Journals (Sweden)

    Angela M White

    Full Text Available As a result of past practices, many of the dry coniferous forests of the western United States contain dense, even-aged stands with uncharacteristically high levels of litter and downed woody debris. These changes to the forest have received considerable attention as they elevate concerns regarding the outcome of wildland fire. However, attempts to reduce biomass through fuel reduction (i.e., thinning of trees are often opposed by public interest groups whose objectives include maintaining habitat for species of concern such as the spotted owl, Strix occidentalis, the northern goshawk, Accipiter gentilis, and the Pacific fisher, Martes pennanti. Whether protection of these upper-trophic level species confers adequate conservation of avian forest diversity is unknown.We use a multi-species occurrence model to estimate the habitat associations of 47 avian species detected at 742 sampling locations within an 880-km(2 area in the Sierra Nevada. Our approach, which accounts for variations in detectability of species, estimates occurrence probabilities of all species in a community by linking species occurrence models into one hierarchical community model, thus improving inferences on all species, especially those that are rare or observed infrequently. We address how the avian community is influenced by covariates related to canopy cover, tree size and shrub cover while accounting for the impacts of abiotic variables known to affect species distributions.Environmental parameters estimated through our approach emphasize the importance of within and between stand-level heterogeneity in meeting biodiversity objectives and suggests that many avian species would increase under more open canopy habitat conditions than those favored by umbrella species of high conservation concern. Our results suggest that a more integrated approach that emphasizes maintaining a diversity of habitats across environmental gradients and minimizing urbanization may have a

  11. Conservation of avian diversity in the Sierra Nevada: moving beyond a single-species management focus

    Science.gov (United States)

    White, Angela M.; Zipkin, Elise F.; Manley, Patricia N.; Schlesinger, Matthew D.

    2013-01-01

    Background: As a result of past practices, many of the dry coniferous forests of the western United States contain dense, even-aged stands with uncharacteristically high levels of litter and downed woody debris. These changes to the forest have received considerable attention as they elevate concerns regarding the outcome of wildland fire. However, attempts to reduce biomass through fuel reduction (i.e., thinning of trees) are often opposed by public interest groups whose objectives include maintaining habitat for species of concern such as the spotted owl, Strix occidentalis, the northern goshawk, Accipiter gentilis, and the Pacific fisher, Martes pennanti. Whether protection of these upper-trophic level species confers adequate conservation of avian forest diversity is unknown. Methodology and Principal Findings: We use a multi-species occurrence model to estimate the habitat associations of 47 avian species detected at 742 sampling locations within an 880-km2 area in the Sierra Nevada. Our approach, which accounts for variations in detectability of species, estimates occurrence probabilities of all species in a community by linking species occurrence models into one hierarchical community model, thus improving inferences on all species, especially those that are rare or observed infrequently. We address how the avian community is influenced by covariates related to canopy cover, tree size and shrub cover while accounting for the impacts of abiotic variables known to affect species distributions. Conclusions and Significance: Environmental parameters estimated through our approach emphasize the importance of within and between stand-level heterogeneity in meeting biodiversity objectives and suggests that many avian species would increase under more open canopy habitat conditions than those favored by umbrella species of high conservation concern. Our results suggest that a more integrated approach that emphasizes maintaining a diversity of habitats across

  12. Using latent selection difference to model persistence in a declining population.

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    Mara E Erickson

    Full Text Available Population persistence is a direct measure of the viability of a population. Monitoring the distribution of declining populations or subpopulations over time can yield estimates of persistence, which we show can be modeled as a latent selection difference (LSD contrasting attributes of sites where populations have persisted versus those that have not. Predicted persistence can be modeled with predictor covariates to identify factors correlated with species persistence. We demonstrate how to model persistence based on changes in occupancy that can include adjustments for detection probability. Using a known historical distribution of the western grebe (Aechmophorus occidentalis, we adapted methods originally developed for occupancy modeling to evaluate how environmental covariates including emergent vegetation and human developments have affected western grebe persistence in Alberta. The relative probability of persistence was correlated with the extent of shoreline bulrush (Scirpus lacustris, which is important vegetation for nesting cover. We also documented that western grebe populations were less likely to persist on lakes in the boreal forest, primarily located on the northern boundary of the species' range. Factors influencing occupancy were different than those determining persistence by western grebes; persistence and occupancy were not correlated. Persistence was more likely on lakes with recreational development, reflecting reliance by grebes on the larger, fish-bearing waterbodies that also are attractive for lakeshore development. Unfortunately, the correlation with recreational development on Alberta's lakes puts grebes at risk for loss of brood-rearing habitats--primary threats to altricial birds--if steps are not taken to prevent disturbance to bulrush stands. Identifying factors related to the persistence of a species--especially one in decline--is a fundamental step in conservation management.

  13. Coupling Satellite Data with Species Distribution and Connectivity Models as a Tool for Environmental Management and Planning in Matrix-Sensitive Species

    Science.gov (United States)

    Rödder, Dennis; Nekum, Sven; Cord, Anna F.; Engler, Jan O.

    2016-07-01

    Climate change and anthropogenic habitat fragmentation are considered major threats for global biodiversity. As a direct consequence, connectivity is increasingly disrupted in many species, which might have serious consequences that could ultimately lead to the extinction of populations. Although a large number of reserves and conservation sites are designated and protected by law, potential habitats acting as inter-population connectivity corridors are, however, mostly ignored in the common practice of environmental planning. In most cases, this is mainly caused by a lack of quantitative measures of functional connectivity available for the planning process. In this study, we highlight the use of fine-scale potential connectivity models (PCMs) derived from multispectral satellite data for the quantification of spatially explicit habitat corridors for matrix-sensitive species of conservation concern. This framework couples a species distribution model with a connectivity model in a two-step framework, where suitability maps from step 1 are transformed into maps of landscape resistance in step 2 filtered by fragmentation thresholds. We illustrate the approach using the sand lizard ( Lacerta agilis L.) in the metropolitan area of Cologne, Germany, as a case study. Our model proved to be well suited to identify connected as well as completely isolated populations within the study area. Furthermore, due to its fine resolution, the PCM was also able to detect small linear structures known to be important for sand lizards' inter-population connectivity such as railroad embankments. We discuss the applicability and possible implementation of PCMs to overcome shortcomings in the common practice of environmental impact assessments.

  14. Comparing climate change and species invasions as drivers of coldwater fish population extirpations.

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    Sapna Sharma

    Full Text Available Species are influenced by multiple environmental stressors acting simultaneously. Our objective was to compare the expected effects of climate change and invasion of non-indigenous rainbow smelt (Osmerus mordax on cisco (Coregonus artedii population extirpations at a regional level. We assembled a database of over 13,000 lakes in Wisconsin, USA, summarising fish occurrence, lake morphology, water chemistry, and climate. We used A1, A2, and B1 scenarios from the Intergovernmental Panel on Climate Change (IPCC of future temperature conditions for 15 general circulation models in 2046-2065 and 2081-2100 totalling 78 projections. Logistic regression indicated that cisco tended to occur in cooler, larger, and deeper lakes. Depending upon the amount of warming, 25-70% of cisco populations are predicted to be extirpated by 2100. In addition, cisco are influenced by the invasion of rainbow smelt, which prey on young cisco. Projecting current estimates of rainbow smelt spread and impact into the future will result in the extirpation of about 1% of cisco populations by 2100 in Wisconsin. Overall, the effect of climate change is expected to overshadow that of species invasion as a driver of coldwater fish population extirpations. Our results highlight the potentially dominant role of climate change as a driver of biotic change.

  15. Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii Populations

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    Puji Rianti

    2015-10-01

    Full Text Available The hypervariable region I of mitochondrial DNA has frequently been used to distinguish among populations, in particular in species with strong female philopatry. In such cases, populations are expected to diverge rapidly for hypervariable region I markers because of the smaller effective population size and thus increased genetic drift. This rapid divergence leads to the accumulation of mutations exclusively found in one population, which may serve as diagnostic single nucleotide polymorphisms (SNPs. To date, diagnostic SNPs distinctive to Sumatran orangutan populations have not yet been described. However, given the continuously declining numbers of Sumatran orangutans, this information can be vital for effective conservation measures, especially regarding reintroductions of orangutans in rehabilitation centers. Phylogenetic analyses of 54 samples of Sumatran orangutans from nine sampling sites with good provenance, we found five major clades and a total of 20 haplotypes. We propose a total of 52 diagnostic SNPs that are specific to Sumatran orangutan populations. Data can be used to develop restriction fragment length polymorphism assays to carry out genetic assignments using basic laboratory equipment to assign Sumatran orangutan to their population of origin.

  16. Exploiting ecology in drug pulse sequences in favour of population reduction.

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    Marianne Bauer

    2017-09-01

    Full Text Available A deterministic population dynamics model involving birth and death for a two-species system, comprising a wild-type and more resistant species competing via logistic growth, is subjected to two distinct stress environments designed to mimic those that would typically be induced by temporal variation in the concentration of a drug (antibiotic or chemotherapeutic as it permeates through the population and is progressively degraded. Different treatment regimes, involving single or periodical doses, are evaluated in terms of the minimal population size (a measure of the extinction probability, and the population composition (a measure of the selection pressure for resistance or tolerance during the treatment. We show that there exist timescales over which the low-stress regime is as effective as the high-stress regime, due to the competition between the two species. For multiple periodic treatments, competition can ensure that the minimal population size is attained during the first pulse when the high-stress regime is short, which implies that a single short pulse can be more effective than a more protracted regime. Our results suggest that when the duration of the high-stress environment is restricted, a treatment with one or multiple shorter pulses can produce better outcomes than a single long treatment. If ecological competition is to be exploited for treatments, it is crucial to determine these timescales, and estimate for the minimal population threshold that suffices for extinction. These parameters can be quantified by experiment.

  17. Prioritizing Avian Species for Their Risk of Population-Level Consequences from Wind Energy Development.

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    Julie A Beston

    Full Text Available Recent growth in the wind energy industry has increased concerns about its impacts on wildlife populations. Direct impacts of wind energy include bird and bat collisions with turbines whereas indirect impacts include changes in wildlife habitat and behavior. Although many species may withstand these effects, species that are long-lived with low rates of reproduction, have specialized habitat preferences, or are attracted to turbines may be more prone to declines in population abundance. We developed a prioritization system to identify the avian species most likely to experience population declines from wind facilities based on their current conservation status and their expected risk from turbines. We developed 3 metrics of turbine risk that incorporate data on collision fatalities at wind facilities, population size, life history, species' distributions relative to turbine locations, number of suitable habitat types, and species' conservation status. We calculated at least 1 measure of turbine risk for 428 avian species that breed in the United States. We then simulated 100,000 random sets of cutoff criteria (i.e., the metric values used to assign species to different priority categories for each turbine risk metric and for conservation status. For each set of criteria, we assigned each species a priority score and calculated the average priority score across all sets of criteria. Our prioritization system highlights both species that could potentially experience population decline caused by wind energy and species at low risk of population decline. For instance, several birds of prey, such as the long-eared owl, ferruginous hawk, Swainson's hawk, and golden eagle, were at relatively high risk of population decline across a wide variety of cutoff values, whereas many passerines were at relatively low risk of decline. This prioritization system is a first step that will help researchers, conservationists, managers, and industry target future

  18. Prioritizing Avian Species for Their Risk of Population-Level Consequences from Wind Energy Development.

    Science.gov (United States)

    Beston, Julie A; Diffendorfer, Jay E; Loss, Scott R; Johnson, Douglas H

    2016-01-01

    Recent growth in the wind energy industry has increased concerns about its impacts on wildlife populations. Direct impacts of wind energy include bird and bat collisions with turbines whereas indirect impacts include changes in wildlife habitat and behavior. Although many species may withstand these effects, species that are long-lived with low rates of reproduction, have specialized habitat preferences, or are attracted to turbines may be more prone to declines in population abundance. We developed a prioritization system to identify the avian species most likely to experience population declines from wind facilities based on their current conservation status and their expected risk from turbines. We developed 3 metrics of turbine risk that incorporate data on collision fatalities at wind facilities, population size, life history, species' distributions relative to turbine locations, number of suitable habitat types, and species' conservation status. We calculated at least 1 measure of turbine risk for 428 avian species that breed in the United States. We then simulated 100,000 random sets of cutoff criteria (i.e., the metric values used to assign species to different priority categories) for each turbine risk metric and for conservation status. For each set of criteria, we assigned each species a priority score and calculated the average priority score across all sets of criteria. Our prioritization system highlights both species that could potentially experience population decline caused by wind energy and species at low risk of population decline. For instance, several birds of prey, such as the long-eared owl, ferruginous hawk, Swainson's hawk, and golden eagle, were at relatively high risk of population decline across a wide variety of cutoff values, whereas many passerines were at relatively low risk of decline. This prioritization system is a first step that will help researchers, conservationists, managers, and industry target future study and management

  19. [A Cellular Automata Model for a Community Comprising Two Plant Species of Different Growth Forms].

    Science.gov (United States)

    Frolov, P V; Zubkova, E V; Komarov, A S

    2015-01-01

    A cellular automata computer model for the interactions between two plant species of different growth forms--the lime hairgrass Deschampsia caespitosa (L.) P. Beauv., a sod cereal, and the moneywort Lysimachia nummularia L., a ground creeping perennial herb--is considered. Computer experiments on the self-maintenance of the populations of each species against the background of a gradual increase in the share of randomly eliminated individuals, coexistence of the populations of two species, and the effect of the phytogenous field have been conducted. As has been shown, all the studied factors determine the number of individuals and self-sustainability of the simulated populations by the degree of their impact. The limits of action have been determined for individual factors; within these limits, the specific features in plant reproduction and dispersal provide sustainable coexistence of the simulated populations. It has been demonstrated that the constructed model allows for studying the long-term developmental dynamics of the plants belonging to the selected growth forms.

  20. The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling.

    Science.gov (United States)

    Wisz, Mary Susanne; Pottier, Julien; Kissling, W Daniel; Pellissier, Loïc; Lenoir, Jonathan; Damgaard, Christian F; Dormann, Carsten F; Forchhammer, Mads C; Grytnes, John-Arvid; Guisan, Antoine; Heikkinen, Risto K; Høye, Toke T; Kühn, Ingolf; Luoto, Miska; Maiorano, Luigi; Nilsson, Marie-Charlotte; Normand, Signe; Öckinger, Erik; Schmidt, Niels M; Termansen, Mette; Timmermann, Allan; Wardle, David A; Aastrup, Peter; Svenning, Jens-Christian

    2013-02-01

    Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km(2) to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally

  1. Assessing local population vulnerability to wind energy development with branching process models: an application to wind energy development

    Science.gov (United States)

    Erickson, Richard A.; Eager, Eric A.; Stanton, Jessica C.; Beston, Julie A.; Diffendorfer, James E.; Thogmartin, Wayne E.

    2015-01-01

    Quantifying the impact of anthropogenic development on local populations is important for conservation biology and wildlife management. However, these local populations are often subject to demographic stochasticity because of their small population size. Traditional modeling efforts such as population projection matrices do not consider this source of variation whereas individual-based models, which include demographic stochasticity, are computationally intense and lack analytical tractability. One compromise between approaches is branching process models because they accommodate demographic stochasticity and are easily calculated. These models are known within some sub-fields of probability and mathematical ecology but are not often applied in conservation biology and applied ecology. We applied branching process models to quantitatively compare and prioritize species locally vulnerable to the development of wind energy facilities. Specifically, we examined species vulnerability using branching process models for four representative species: A cave bat (a long-lived, low fecundity species), a tree bat (short-lived, moderate fecundity species), a grassland songbird (a short-lived, high fecundity species), and an eagle (a long-lived, slow maturation species). Wind turbine-induced mortality has been observed for all of these species types, raising conservation concerns. We simulated different mortality rates from wind farms while calculating local extinction probabilities. The longer-lived species types (e.g., cave bats and eagles) had much more pronounced transitions from low extinction risk to high extinction risk than short-lived species types (e.g., tree bats and grassland songbirds). High-offspring-producing species types had a much greater variability in baseline risk of extinction than the lower-offspring-producing species types. Long-lived species types may appear stable until a critical level of incidental mortality occurs. After this threshold, the risk of

  2. A stochastic step model of replicative senescence explains ROS production rate in ageing cell populations.

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    Conor Lawless

    Full Text Available Increases in cellular Reactive Oxygen Species (ROS concentration with age have been observed repeatedly in mammalian tissues. Concomitant increases in the proportion of replicatively senescent cells in ageing mammalian tissues have also been observed. Populations of mitotic human fibroblasts cultured in vitro, undergoing transition from proliferation competence to replicative senescence are useful models of ageing human tissues. Similar exponential increases in ROS with age have been observed in this model system. Tracking individual cells in dividing populations is difficult, and so the vast majority of observations have been cross-sectional, at the population level, rather than longitudinal observations of individual cells.One possible explanation for these observations is an exponential increase in ROS in individual fibroblasts with time (e.g. resulting from a vicious cycle between cellular ROS and damage. However, we demonstrate an alternative, simple hypothesis, equally consistent with these observations which does not depend on any gradual increase in ROS concentration: the Stochastic Step Model of Replicative Senescence (SSMRS. We also demonstrate that, consistent with the SSMRS, neither proliferation-competent human fibroblasts of any age, nor populations of hTERT overexpressing human fibroblasts passaged beyond the Hayflick limit, display high ROS concentrations. We conclude that longitudinal studies of single cells and their lineages are now required for testing hypotheses about roles and mechanisms of ROS increase during replicative senescence.

  3. A stochastic step model of replicative senescence explains ROS production rate in ageing cell populations.

    Science.gov (United States)

    Lawless, Conor; Jurk, Diana; Gillespie, Colin S; Shanley, Daryl; Saretzki, Gabriele; von Zglinicki, Thomas; Passos, João F

    2012-01-01

    Increases in cellular Reactive Oxygen Species (ROS) concentration with age have been observed repeatedly in mammalian tissues. Concomitant increases in the proportion of replicatively senescent cells in ageing mammalian tissues have also been observed. Populations of mitotic human fibroblasts cultured in vitro, undergoing transition from proliferation competence to replicative senescence are useful models of ageing human tissues. Similar exponential increases in ROS with age have been observed in this model system. Tracking individual cells in dividing populations is difficult, and so the vast majority of observations have been cross-sectional, at the population level, rather than longitudinal observations of individual cells.One possible explanation for these observations is an exponential increase in ROS in individual fibroblasts with time (e.g. resulting from a vicious cycle between cellular ROS and damage). However, we demonstrate an alternative, simple hypothesis, equally consistent with these observations which does not depend on any gradual increase in ROS concentration: the Stochastic Step Model of Replicative Senescence (SSMRS). We also demonstrate that, consistent with the SSMRS, neither proliferation-competent human fibroblasts of any age, nor populations of hTERT overexpressing human fibroblasts passaged beyond the Hayflick limit, display high ROS concentrations. We conclude that longitudinal studies of single cells and their lineages are now required for testing hypotheses about roles and mechanisms of ROS increase during replicative senescence.

  4. Analysis of a Fishery Model with two competing prey species in the presence of a predator species for Optimal Harvesting

    Science.gov (United States)

    Sutimin; Khabibah, Siti; Munawwaroh, Dita Anis

    2018-02-01

    A harvesting fishery model is proposed to analyze the effects of the presence of red devil fish population, as a predator in an ecosystem. In this paper, we consider an ecological model of three species by taking into account two competing species and presence of a predator (red devil), the third species, which incorporates the harvesting efforts of each fish species. The stability of the dynamical system is discussed and the existence of biological and bionomic equilibrium is examined. The optimal harvest policy is studied and the solution is derived in the equilibrium case applying Pontryagin's maximal principle. The simulation results is presented to simulate the dynamical behavior of the model and show that the optimal equilibrium solution is globally asymptotically stable. The results show that the optimal harvesting effort is obtained regarding to bionomic and biological equilibrium.

  5. Population Trends of Central European Montane Birds Provide Evidence for Adverse Impacts of Climate Change on High-Altitude Species.

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    Jiří Flousek

    Full Text Available Climate change is among the most important global threats to biodiversity and mountain areas are supposed to be under especially high pressure. Although recent modelling studies suggest considerable future range contractions of montane species accompanied with increased extinction risk, data allowing to test actual population consequences of the observed climate changes and identifying traits associated to their adverse impacts are very scarce. To fill this knowledge gap, we estimated long-term population trends of montane birds from 1984 to 2011 in a central European mountain range, the Giant Mountains (Krkonoše, where significant warming occurred over this period. We then related the population trends to several species' traits related to the climate change effects. We found that the species breeding in various habitats at higher altitudes had more negative trends than species breeding at lower altitudes. We also found that the species moved upwards as a response to warming climate, and these altitudinal range shifts were associated with more positive population trends at lower altitudes than at higher altitudes. Moreover, long-distance migrants declined more than residents or species migrating for shorter distances. Taken together, these results indicate that the climate change, besides other possible environmental changes, already influences populations of montane birds with particularly adverse impacts on high-altitude species such as water pipit (Anthus spinoletta. It is evident that the alpine species, predicted to undergo serious climatically induced range contractions due to warming climate in the future, already started moving along this trajectory.

  6. The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species.

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    Thibaud Rougier

    Full Text Available Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa, an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5. We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local

  7. Efficiency of green manure species on the population of reniform nematode

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    Cristiane Gonçalves Gardiano

    2014-02-01

    Full Text Available The objective of this study was to evaluate the growing of soil improving crops on the population of Rotylenchulus reniformis in naturally infested soil. It was evaluated the effect of 6 species of plants as cover crops in winter and 13 summer species and a fallow treatment on the nematode population under greenhouse. After 60 days, the root system was collected. Then, a sample of soil was taken in order to extract juveniles from the soil and quantification the final population of the pathogen in each pot for determining of the reproduction factor (RF. Fallow and all winter species of green manure, except hairy vetch, reduced the population of R. reniformis after cultivation in infested soil, in comparison to the control. Regarding summer cover crops, it was observed that sorghum ‘SI03204’ (Sorghum vulgare, millet ‘BRS1501’ (Pennisetum glaucum, Brachiaria ruziziensis, finger millet (Eleusine coracana, estylo ‘Campo Grande’ (Stylosanthes capitata x S. macrocephala, peanut ‘IAC Tatu ST’ (Arachis hypogaea and dwarf velvet bean (Mucuna deeringiana reduced the population of R. reniformis, when compared to the control, could be used in the management of this nematode.

  8. Species-free species distribution models describe macroecological properties of protected area networks.

    Science.gov (United States)

    Robinson, Jason L; Fordyce, James A

    2017-01-01

    Among the greatest challenges facing the conservation of plants and animal species in protected areas are threats from a rapidly changing climate. An altered climate creates both challenges and opportunities for improving the management of protected areas in networks. Increasingly, quantitative tools like species distribution modeling are used to assess the performance of protected areas and predict potential responses to changing climates for groups of species, within a predictive framework. At larger geographic domains and scales, protected area network units have spatial geoclimatic properties that can be described in the gap analysis typically used to measure or aggregate the geographic distributions of species (stacked species distribution models, or S-SDM). We extend the use of species distribution modeling techniques in order to model the climate envelope (or "footprint") of individual protected areas within a network of protected areas distributed across the 48 conterminous United States and managed by the US National Park System. In our approach we treat each protected area as the geographic range of a hypothetical endemic species, then use MaxEnt and 5 uncorrelated BioClim variables to model the geographic distribution of the climatic envelope associated with each protected area unit (modeling the geographic area of park units as the range of a species). We describe the individual and aggregated climate envelopes predicted by a large network of 163 protected areas and briefly illustrate how macroecological measures of geodiversity can be derived from our analysis of the landscape ecological context of protected areas. To estimate trajectories of change in the temporal distribution of climatic features within a protected area network, we projected the climate envelopes of protected areas in current conditions onto a dataset of predicted future climatic conditions. Our results suggest that the climate envelopes of some parks may be locally unique or have

  9. Stochastic population oscillations in spatial predator-prey models

    International Nuclear Information System (INIS)

    Taeuber, Uwe C

    2011-01-01

    It is well-established that including spatial structure and stochastic noise in models for predator-prey interactions invalidates the classical deterministic Lotka-Volterra picture of neutral population cycles. In contrast, stochastic models yield long-lived, but ultimately decaying erratic population oscillations, which can be understood through a resonant amplification mechanism for density fluctuations. In Monte Carlo simulations of spatial stochastic predator-prey systems, one observes striking complex spatio-temporal structures. These spreading activity fronts induce persistent correlations between predators and prey. In the presence of local particle density restrictions (finite prey carrying capacity), there exists an extinction threshold for the predator population. The accompanying continuous non-equilibrium phase transition is governed by the directed-percolation universality class. We employ field-theoretic methods based on the Doi-Peliti representation of the master equation for stochastic particle interaction models to (i) map the ensuing action in the vicinity of the absorbing state phase transition to Reggeon field theory, and (ii) to quantitatively address fluctuation-induced renormalizations of the population oscillation frequency, damping, and diffusion coefficients in the species coexistence phase.

  10. Including cetaceans in multi-species assessment models using strandings data: why, how and what can we do about it?

    Directory of Open Access Journals (Sweden)

    Camilo Saavedra

    2014-07-01

    due to lack of good information because, unlike the case of commercial fish stocks, usually there are no timeseries of abundance estimates available and the biological information available has been derived from the examination of stranded and/or bycatch individuals which could generate biased estimates. Common dolphin is the more abundant species of small cetacean in the Atlantic coast of the Iberian Peninsula and for which more biological information is available. For this reason, we have used this species as an example to explain our approach to obtain estimates of all the biological parameters needed to build a cetacean population model from strandings data. Southern European hake stock is distributed from Gulf of Biscay to Strait of Gibraltar, along Atlantic coast of the Iberian Peninsula, and thus the common dolphin population we will try to model is the one which lies in this area, although it is considered that there is a single common dolphin population is continuous throughout the European Atlantic coast (Natoli, 2008. Due to their protected status, no timeseries of catches neither fishing biological samples exist in the area, in contrast as in commercial fish species. Therefore, the major source of biological information is derived from strandings, mainly collected by experienced personnel from the “Coordinadora para o Estudio dos Mamíferos Mariños” (CEMMA operating in Galicia (Northwest of Spain since 1990. From these data we have derived the direct and indirect information required for our model. However, only the following parameters: maximum and minimum dolphin length and weight, sex-ratio and proportion of dead dolphins exhibiting bycatch signs can be used without further data processing. From these parameters, the length-weight relationship can also be easily calculated for both males and females, in our case, by fitting a logarithmic regression. Nonetheless, to fit a growth curve is necessary to know the age of each stranded dolphin and

  11. Simulation of population response to ionizing radiation in an ecosystem with a limiting resource – Model and analytical solutions

    International Nuclear Information System (INIS)

    Sazykina, Tatiana G.; Kryshev, Alexander I.

    2016-01-01

    A dynamic mathematical model is formulated, predicting the development of radiation effects in a generic animal population, inhabiting an elemental ecosystem ‘population-limiting resource’. Differential equations of the model describe the dynamic responses to radiation damage of the following population characteristics: gross biomass; intrinsic fractions of healthy and reversibly damaged tissues in biomass; intrinsic concentrations of the self-repairing pool and the growth factor; and amount of the limiting resource available in the environment. Analytical formulae are found for the steady states of model variables as non-linear functions of the dose rate of chronic radiation exposure. Analytical solutions make it possible to predict the expected severity of radiation effects in a model ecosystem, including such endpoints as morbidity, mortality, life shortening, biosynthesis, and population biomass. Model parameters are selected from species data on lifespan, physiological growth and mortality rates, and individual radiosensitivity. Thresholds for population extinction can be analytically calculated for different animal species, examples are provided for generic mice and wolf populations. The ecosystem model demonstrates a compensatory effect of the environment on the development of radiation effects in wildlife. The model can be employed to construct a preliminary scale ‘radiation exposure-population effects’ for different animal species; species can be identified, which are vulnerable at a population level to chronic radiation exposure. - Highlights: • Mathematical model is formulated predicting radiation effects in elemental ecosystem. • Analytical formulae are found for steady states of variables as functions of exposure. • Severity of radiation effects are calculated, including population extinction. • Model parameterization is made for generic mice and wolf populations.

  12. Estimation of effective population size in continuously distributed populations: There goes the neighborhood

    Science.gov (United States)

    M. C. Neel; K. McKelvey; N. Ryman; M. W. Lloyd; R. Short Bull; F. W. Allendorf; M. K. Schwartz; R. S. Waples

    2013-01-01

    Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating...

  13. Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas.

    Science.gov (United States)

    Paterno, Marta; Schiavina, Marcello; Aglieri, Giorgio; Ben Souissi, Jamila; Boscari, Elisa; Casagrandi, Renato; Chassanite, Aurore; Chiantore, Mariachiara; Congiu, Leonardo; Guarnieri, Giuseppe; Kruschel, Claudia; Macic, Vesna; Marino, Ilaria A M; Papetti, Chiara; Patarnello, Tomaso; Zane, Lorenzo; Melià, Paco

    2017-04-01

    Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus , focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic-Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic-Ionian locations indicates species-specific differences in genetic connectivity patterns and warns against generalizing single-species results to the entire community of rocky shore habitats.

  14. Single-limb force data for two lemur species while vertically clinging.

    Science.gov (United States)

    Johnson, Laura E; Hanna, Jandy; Schmitt, Daniel

    2015-11-01

    Vertical clinging and climbing have been integral to hypotheses about primate origins, yet little is known about how an animal with nails instead of claws resists gravity while on large, vertical, and cylindrical substrates. Here we test models of how force is applied to maintain posture, predicting (1) the shear component force (Fs ) at the hands will be higher than the feet; (2) the normal component force (Fn ) at the feet will be relatively high compared to the hands; (3) the component force resisting gravity (Fg ) at the feet will be relatively high compared to the hands; (4) species with a high frequency of vertical clinging postures will have low Fg at the hands due to relatively short forelimbs. Using a novel instrumented support, single-limb force data were collected during clinging postures for the hands and feet and compared across limbs and species for Propithecus verreauxi (N = 2), a habitual vertical clinger and leaper, and Varecia variegata (N = 3), a habitual above-branch arboreal quadruped. For both species, hand Fs were significantly higher than at the feet and Fn and Fg at the feet were significantly higher than at the hands. Between species, P. verreauxi has relatively low Fg at the hands and Fn at the feet than V. vareigata. These results support previous models and show that hindlimb loading dominance, characteristic of primate locomotion, is found during clinging behaviors and may allow the forelimbs to be used for foraging while clinging. These findings provide insight into selective pressures on force distribution in primates and primate locomotor evolution. © 2015 Wiley Periodicals, Inc.

  15. Hierarchical species distribution models

    Science.gov (United States)

    Hefley, Trevor J.; Hooten, Mevin B.

    2016-01-01

    Determining the distribution pattern of a species is important to increase scientific knowledge, inform management decisions, and conserve biodiversity. To infer spatial and temporal patterns, species distribution models have been developed for use with many sampling designs and types of data. Recently, it has been shown that count, presence-absence, and presence-only data can be conceptualized as arising from a point process distribution. Therefore, it is important to understand properties of the point process distribution. We examine how the hierarchical species distribution modeling framework has been used to incorporate a wide array of regression and theory-based components while accounting for the data collection process and making use of auxiliary information. The hierarchical modeling framework allows us to demonstrate how several commonly used species distribution models can be derived from the point process distribution, highlight areas of potential overlap between different models, and suggest areas where further research is needed.

  16. Quantitative occupational risk model: Single hazard

    International Nuclear Information System (INIS)

    Papazoglou, I.A.; Aneziris, O.N.; Bellamy, L.J.; Ale, B.J.M.; Oh, J.

    2017-01-01

    A model for the quantification of occupational risk of a worker exposed to a single hazard is presented. The model connects the working conditions and worker behaviour to the probability of an accident resulting into one of three types of consequence: recoverable injury, permanent injury and death. Working conditions and safety barriers in place to reduce the likelihood of an accident are included. Logical connections are modelled through an influence diagram. Quantification of the model is based on two sources of information: a) number of accidents observed over a period of time and b) assessment of exposure data of activities and working conditions over the same period of time and the same working population. Effectiveness of risk reducing measures affecting the working conditions, worker behaviour and/or safety barriers can be quantified through the effect of these measures on occupational risk. - Highlights: • Quantification of occupational risk from a single hazard. • Influence diagram connects working conditions, worker behaviour and safety barriers. • Necessary data include the number of accidents and the total exposure of worker • Effectiveness of risk reducing measures is quantified through the impact on the risk • An example illustrates the methodology.

  17. Bayesian modeling of recombination events in bacterial populations

    Directory of Open Access Journals (Sweden)

    Dowson Chris

    2008-10-01

    Full Text Available Abstract Background We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. Results We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. Conclusion A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/mnf//mate/jc/software/brat.html.

  18. The population of single and binary white dwarfs of the Galactic bulge

    Science.gov (United States)

    Torres, S.; García-Berro, E.; Cojocaru, R.; Calamida, A.

    2018-05-01

    Recent Hubble Space Telescope observations have unveiled the white dwarf cooling sequence of the Galactic bulge. Although the degenerate sequence can be well fitted employing the most up-to-date theoretical cooling sequences, observations show a systematic excess of red objects that cannot be explained by the theoretical models of single carbon-oxygen white dwarfs of the appropriate masses. Here, we present a population synthesis study of the white dwarf cooling sequence of the Galactic bulge that takes into account the populations of both single white dwarfs and binary systems containing at least one white dwarf. These calculations incorporate state-of-the-art cooling sequences for white dwarfs with hydrogen-rich and hydrogen-deficient atmospheres, for both white dwarfs with carbon-oxygen and helium cores, and also take into account detailed prescriptions of the evolutionary history of binary systems. Our Monte Carlo simulator also incorporates all the known observational biases. This allows us to model with a high degree of realism the white dwarf population of the Galactic bulge. We find that the observed excess of red stars can be partially attributed to white dwarf plus main sequence binaries, and to cataclysmic variables or dwarf novae. Our best fit is obtained with a higher binary fraction and an initial mass function slope steeper than standard values, as well as with the inclusion of differential reddening and blending. Our results also show that the possible contribution of double degenerate systems or young and thick-discbulge stars is negligible.

  19. Surfing among species, populations and morphotypes: Inferring boundaries between two species of new world silversides (Atherinopsidae).

    Science.gov (United States)

    González-Castro, Mariano; Rosso, Juan José; Mabragaña, Ezequiel; Díaz de Astarloa, Juan Martín

    2016-01-01

    Atherinopsidae are widespread freshwater and shallow marine fish with singular economic importance. Morphological, genetical and life cycles differences between marine and estuarine populations were already reported in this family, suggesting ongoing speciation. Also, coexistence and interbreeding between closely related species were documented. The aim of this study was to infer boundaries among: (A) Odontesthes bonariensis and O. argentinensis at species level, and intermediate morphs; (B) the population of O. argentinensis of Mar Chiquita Lagoon and its marine conspecifics. To achieve this, we integrated, meristic, Geometrics Morphometrics and DNA Barcode approaches. Four groups were discriminated and subsequently characterized according to their morphological traits, shape and meristic characters. No shared haplotypes between O. bonariensis and O. argentinensis were found. Significative-meristic and body shape differences between the Mar Chiquita and marine individuals of O. argentinensis were found, suggesting they behave as well differentiated populations, or even incipient ecological species. The fact that the Odontesthes morphotypes shared haplotypes with both, O. argentinensis and O. bonariensis, but also possess meristic and morphometric distinctive traits open new questions related to the origin of this morphogroup. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  20. Prioritizing avian species for their risk of population-level consequences from wind energy development

    Science.gov (United States)

    Beston, Julie A.; Diffendorfer, James E.; Loss, Scott; Johnson, Douglas H.

    2016-01-01

    Recent growth in the wind energy industry has increased concerns about its impacts on wildlife populations. Direct impacts of wind energy include bird and bat collisions with turbines whereas indirect impacts include changes in wildlife habitat and behavior. Although many species may withstand these effects, species that are long-lived with low rates of reproduction, have specialized habitat preferences, or are attracted to turbines may be more prone to declines in population abundance. We developed a prioritization system to identify the avian species most likely to experience population declines from wind facilities based on their current conservation status and their expected risk from turbines. We developed 3 metrics of turbine risk that incorporate data on collision fatalities at wind facilities, population size, life history, species’ distributions relative to turbine locations, number of suitable habitat types, and species’ conservation status. We calculated at least 1 measure of turbine risk for 428 avian species that breed in the United States. We then simulated 100,000 random sets of cutoff criteria (i.e., the metric values used to assign species to different priority categories) for each turbine risk metric and for conservation status. For each set of criteria, we assigned each species a priority score and calculated the average priority score across all sets of criteria. Our prioritization system highlights both species that could potentially experience population decline caused by wind energy and species at low risk of population decline. For instance, several birds of prey, such as the long-eared owl, ferruginous hawk, Swainson’s hawk, and golden eagle, were at relatively high risk of population decline across a wide variety of cutoff values, whereas many passerines were at relatively low risk of decline. This prioritization system is a first step that will help researchers, conservationists, managers, and industry target future study and

  1. Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective

    Science.gov (United States)

    Bayramoglu, Bihter; Toubiana, David; van Vliet, Simon; Inglis, R. Fredrik; Shnerb, Nadav; Gillor, Osnat

    2017-02-01

    Production of public goods in biological systems is often a collaborative effort that may be detrimental to the producers. It is therefore sustainable only if a small fraction of the population shoulders the cost while the majority reap the benefits. We modelled this scenario using Escherichia coli populations producing colicins, an antibiotic that kills producer cells’ close relatives. Colicin expression is a costly trait, and it has been proposed that only a small fraction of the population actively expresses the antibiotic. Colicinogenic populations were followed at the single-cell level using time-lapse microscopy, and showed two distinct, albeit dynamic, subpopulations: the majority silenced colicin expression, while a small fraction of elongated, slow-growing cells formed colicin-expressing hotspots, placing a significant burden on expressers. Moreover, monitoring lineages of individual colicinogenic cells showed stochastic switching between expressers and non-expressers. Hence, colicin expressers may be engaged in risk-reducing strategies—or bet-hedging—as they balance the cost of colicin production with the need to repel competitors. To test the bet-hedging strategy in colicin-mediated interactions, competitions between colicin-sensitive and producer cells were simulated using a numerical model, demonstrating a finely balanced expression range that is essential to sustaining the colicinogenic population.

  2. Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes

    Directory of Open Access Journals (Sweden)

    Bachtrog Doris

    2008-12-01

    Full Text Available Abstract Background Adaptive protein evolution is common in several Drosophila species investigated. Some studies point to very weak selection operating on amino-acid mutations, with average selection intensities on the order of Nes ~ 5 in D. melanogaster and D. simulans. Species with lower effective population sizes should undergo less adaptation since they generate fewer mutations and selection is ineffective on a greater proportion of beneficial mutations. Results Here I study patterns of polymorphism and divergence at 91 X-linked loci in D. miranda, a species with a roughly 5-fold smaller effective population size than D. melanogaster. Surprisingly, I find a similar fraction of amino-acid mutations being driven to fixation by positive selection in D. miranda and D. melanogaster. Genes with higher rates of amino-acid evolution show lower levels of neutral diversity, a pattern predicted by recurrent adaptive protein evolution. I fit a hitchhiking model to patterns of polymorphism in D. miranda and D. melanogaster and estimate an order of magnitude higher selection coefficients for beneficial mutations in D. miranda. Conclusion This analysis suggests that effective population size may not be a major determinant in rates of protein adaptation. Instead, adaptation may not be mutation-limited, or the distribution of fitness effects for beneficial mutations might differ vastly between different species or populations. Alternative explanation such as biases in estimating the fraction of beneficial mutations or slightly deleterious mutation models are also discussed.

  3. Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats.

    Science.gov (United States)

    Esselstyn, Jacob A; Evans, Ben J; Sedlock, Jodi L; Anwarali Khan, Faisal Ali; Heaney, Lawrence R

    2012-09-22

    Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N(e)) and speciation rate (SR; per lineage per million years) was less than or equal to 10(5), while interspecific variation in N(e) was twofold or less. However, at higher but also biologically relevant values of N(e) × SR and when N(e) varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N(e), SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.

  4. Asymmetric biotic interactions and abiotic niche differences revealed by a dynamic joint species distribution model.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Schliep, Erin M; Schaeffer, Robert N; Orians, Colin M; Orwig, David A; Preisser, Evan L

    2018-05-01

    A species' distribution and abundance are determined by abiotic conditions and biotic interactions with other species in the community. Most species distribution models correlate the occurrence of a single species with environmental variables only, and leave out biotic interactions. To test the importance of biotic interactions on occurrence and abundance, we compared a multivariate spatiotemporal model of the joint abundance of two invasive insects that share a host plant, hemlock woolly adelgid (HWA; Adelges tsugae) and elongate hemlock scale (EHS; Fiorina externa), to independent models that do not account for dependence among co-occurring species. The joint model revealed that HWA responded more strongly to abiotic conditions than EHS. Additionally, HWA appeared to predispose stands to subsequent increase of EHS, but HWA abundance was not strongly dependent on EHS abundance. This study demonstrates how incorporating spatial and temporal dependence into a species distribution model can reveal the dependence of a species' abundance on other species in the community. Accounting for dependence among co-occurring species with a joint distribution model can also improve estimation of the abiotic niche for species affected by interspecific interactions. © 2018 by the Ecological Society of America.

  5. Habitat Modeling of Alien Plant Species at Varying Levels of Occupancy

    Directory of Open Access Journals (Sweden)

    Jennifer A. Brown

    2012-09-01

    Full Text Available Distribution models of invasive plants are very useful tools for conservation management. There are challenges in modeling expanding populations, especially in a dynamic environment, and when data are limited. In this paper, predictive habitat models were assessed for three invasive plant species, at differing levels of occurrence, using two different habitat modeling techniques: logistic regression and maximum entropy. The influence of disturbance, spatial and temporal heterogeneity, and other landscape characteristics is assessed by creating regional level models based on occurrence records from the USDA Forest Service’s Forest Inventory and Analysis database. Logistic regression and maximum entropy models were assessed independently. Ensemble models were developed to combine the predictions of the two analysis approaches to obtain a more robust prediction estimate. All species had strong models with Area Under the receiver operator Curve (AUC of >0.75. The species with the highest occurrence, Ligustrum spp., had the greatest agreement between the models (93%. Lolium arundinaceum had the most disagreement between models at 33% and the lowest AUC values. Overall, the strength of integrative modeling in assessing and understanding habitat modeling was demonstrated.

  6. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species.

    Science.gov (United States)

    Hsiung, Huan-Yi; Huang, Bing-Hong; Chang, Jui-Tse; Huang, Yao-Moan; Huang, Chih-Wei; Liao, Pei-Chun

    2017-01-01

    Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis , which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.

  7. A population memetics approach to cultural evolution in chaffinch song: meme diversity within populations.

    Science.gov (United States)

    Lynch, A; Baker, A J

    1993-04-01

    We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, Canaries) and neighboring continental regions (Morocco, Iberia) by employing a population memetics approach. To quantify variability within populations, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The frequency distribution of memes within populations generally fit a neutral model in which there is an equilibrium between mutation, migration, and drift, which suggests that memes are functionally equivalent. The diversity of memes of single syllables is significantly greater in the Azores compared to all other regions, consistent with higher population densities of chaffinches there. On the other hand, memes of two to five syllables have greater diversity in Atlantic island and Moroccan populations compared to their Iberian counterparts. This higher diversity emanates from a looser syntax and increased recombination in songs, presumably because of relaxed selection for distinctive songs in these peripheral and depauperate avifaunas. We urge comparative population memetic studies of other species of songbirds and predict that they will lead to a formulation of a general theory for the cultural evolution of bird song analogous to population genetics theory for biological traits.

  8. Visual Basic, Excel-based fish population modeling tool - The pallid sturgeon example

    Science.gov (United States)

    Moran, Edward H.; Wildhaber, Mark L.; Green, Nicholas S.; Albers, Janice L.

    2016-02-10

    The model presented in this report is a spreadsheet-based model using Visual Basic for Applications within Microsoft Excel (http://dx.doi.org/10.5066/F7057D0Z) prepared in cooperation with the U.S. Army Corps of Engineers and U.S. Fish and Wildlife Service. It uses the same model structure and, initially, parameters as used by Wildhaber and others (2015) for pallid sturgeon. The difference between the model structure used for this report and that used by Wildhaber and others (2015) is that variance is not partitioned. For the model of this report, all variance is applied at the iteration and time-step levels of the model. Wildhaber and others (2015) partition variance into parameter variance (uncertainty about the value of a parameter itself) applied at the iteration level and temporal variance (uncertainty caused by random environmental fluctuations with time) applied at the time-step level. They included implicit individual variance (uncertainty caused by differences between individuals) within the time-step level.The interface developed for the model of this report is designed to allow the user the flexibility to change population model structure and parameter values and uncertainty separately for every component of the model. This flexibility makes the modeling tool potentially applicable to any fish species; however, the flexibility inherent in this modeling tool makes it possible for the user to obtain spurious outputs. The value and reliability of the model outputs are only as good as the model inputs. Using this modeling tool with improper or inaccurate parameter values, or for species for which the structure of the model is inappropriate, could lead to untenable management decisions. By facilitating fish population modeling, this modeling tool allows the user to evaluate a range of management options and implications. The goal of this modeling tool is to be a user-friendly modeling tool for developing fish population models useful to natural resource

  9. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  10. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  11. Use of Occupancy Models to Evaluate Expert Knowledge-based Species-Habitat Relationships

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    Monica N. Iglecia

    2012-12-01

    Full Text Available Expert knowledge-based species-habitat relationships are used extensively to guide conservation planning, particularly when data are scarce. Purported relationships describe the initial state of knowledge, but are rarely tested. We assessed support in the data for suitability rankings of vegetation types based on expert knowledge for three terrestrial avian species in the South Atlantic Coastal Plain of the United States. Experts used published studies, natural history, survey data, and field experience to rank vegetation types as optimal, suitable, and marginal. We used single-season occupancy models, coupled with land cover and Breeding Bird Survey data, to examine the hypothesis that patterns of occupancy conformed to species-habitat suitability rankings purported by experts. Purported habitat suitability was validated for two of three species. As predicted for the Eastern Wood-Pewee (Contopus virens and Brown-headed Nuthatch (Sitta pusilla, occupancy was strongly influenced by vegetation types classified as "optimal habitat" by the species suitability rankings for nuthatches and wood-pewees. Contrary to predictions, Red-headed Woodpecker (Melanerpes erythrocephalus models that included vegetation types as covariates received similar support by the data as models without vegetation types. For all three species, occupancy was also related to sampling latitude. Our results suggest that covariates representing other habitat requirements might be necessary to model occurrence of generalist species like the woodpecker. The modeling approach described herein provides a means to test expert knowledge-based species-habitat relationships, and hence, help guide conservation planning.

  12. Waterfowl populations of conservation concern: learning from diverse challenges, models, and conservation strategies

    Science.gov (United States)

    Austin, Jane E.; Slattery, Stuart; Clark, Robert G.

    2014-01-01

    There are 30 threatened or endangered species of waterfowl worldwide, and several sub-populations are also threatened. Some of these species occur in North America, and others there are also of conservation concern due to declining population trends and their importance to hunters. Here we review conservation initiatives being undertaken for several of these latter species, along with conservation measures in place in Europe, to seek common themes and approaches that could be useful in developing broad conservation guidelines. While focal species may vary in their life histories, population threats and geopolitical context, most conservation efforts have used a systematic approach to understand factors limiting populations and o identify possible management or policy actions. This approach generally includes a priori identification of plausible hypotheses about population declines or status, incorporation of hypotheses into conceptual or quantitative planning models, and the use of some form of structured decision making and adaptive management to develop and implement conservation actions in the face of many uncertainties. A climate of collaboration among jurisdictions sharing these birds is important to the success of a conservation or management programme. The structured conservation approach exemplified herein provides an opportunity to involve stakeholders at all planning stages, allows for all views to be examined and incorporated into model structures, and yields a format for improved communication, cooperation and learning, which may ultimately be one of the greatest benefits of this strategy.

  13. A Gompertz population model with Allee effect and fuzzy initial values

    Science.gov (United States)

    Amarti, Zenia; Nurkholipah, Nenden Siti; Anggriani, Nursanti; Supriatna, Asep K.

    2018-03-01

    Growth and population dynamics models are important tools used in preparing a good management for society to predict the future of population or species. This has been done by various known methods, one among them is by developing a mathematical model that describes population growth. Models are usually formed into differential equations or systems of differential equations, depending on the complexity of the underlying properties of the population. One example of biological complexity is Allee effect. It is a phenomenon showing a high correlation between very small population size and the mean individual fitness of the population. In this paper the population growth model used is the Gompertz equation model by considering the Allee effect on the population. We explore the properties of the solution to the model numerically using the Runge-Kutta method. Further exploration is done via fuzzy theoretical approach to accommodate uncertainty of the initial values of the model. It is known that an initial value greater than the Allee threshold will cause the solution rises towards carrying capacity asymptotically. However, an initial value smaller than the Allee threshold will cause the solution decreases towards zero asymptotically, which means the population is eventually extinct. Numerical solutions show that modeling uncertain initial value of the critical point A (the Allee threshold) with a crisp initial value could cause the extinction of population of a certain possibilistic degree, depending on the predetermined membership function of the initial value.

  14. Genetic diversity of Kenyan Prosopis populations based on random amplified polymorphic DNA markers

    OpenAIRE

    Muturi, G.M.; Machua, J.M.; Mohren, G.M.J.; Poorter, L.; Gicheru, J.M.; Maina, L.W.

    2012-01-01

    Several Prosopis species and provenances were introduced in Kenya, either as a single event or repeatedly. To date, naturally established Prosopis populations are described as pure species depending on site, despite the aforementioned introduction of several species within some sites. To determine whether naturally established stands consist of a single or mixture of species, six populations from Bamburi, Bura, Isiolo, Marigat, Taveta and Turkwel were compared for relatedness with reference t...

  15. Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species

    Directory of Open Access Journals (Sweden)

    AB Choupina

    Full Text Available Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia, are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal, there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates, as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as “glochidia” hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

  16. Persistence in a single species CSTR model with suspended flocs and wall attached biofilms.

    Science.gov (United States)

    Mašić, Alma; Eberl, Hermann J

    2012-04-01

    We consider a mathematical model for a bacterial population in a continuously stirred tank reactor (CSTR) with wall attachment. This is a modification of the Freter model, in which we model the sessile bacteria as a microbial biofilm. Our analysis indicates that the results of the algebraically simpler original Freter model largely carry over. In a computational simulation study, we find that the vast majority of bacteria in the reactor will eventually be sessile. However, we also find that suspended biomass is relatively more efficient in removing substrate from the reactor than biofilm bacteria.

  17. Mapping National Plant Biodiversity Patterns in South Korea with the MARS Species Distribution Model.

    Directory of Open Access Journals (Sweden)

    Hyeyeong Choe

    Full Text Available Accurate information on the distribution of existing species is crucial to assess regional biodiversity. However, data inventories are insufficient in many areas. We examine the ability of Multivariate Adaptive Regression Splines (MARS multi-response species distribution model to overcome species' data limitations and portray plant species distribution patterns for 199 South Korean plant species. The study models species with two or more observations, examines their contribution to national patterns of species richness, provides a sensitivity analysis of different range threshold cutoff approaches for modeling species' ranges, and presents considerations for species modeling at fine spatial resolution. We ran MARS models for each species and tested four threshold methods to transform occurrence probabilities into presence or absence range maps. Modeled occurrence probabilities were extracted at each species' presence points, and the mean, median, and one standard deviation (SD calculated to define data-driven thresholds. A maximum sum of sensitivity and specificity threshold was also calculated, and the range maps from the four cutoffs were tested using independent plant survey data. The single SD values were the best threshold tested for minimizing omission errors and limiting species ranges to areas where the associated occurrence data were correctly classed. Eight individual species range maps for rare plant species were identified that are potentially affected by resampling predictor variables to fine spatial scales. We portray spatial patterns of high species richness by assessing the combined range maps from three classes of species: all species, endangered and endemic species, and range-size rarity of all species, which could be used in conservation planning for South Korea. The MARS model is promising for addressing the common problem of few species occurrence records. However, projected species ranges are highly dependent on the

  18. Predicting the effect of ionising radiation on biological populations: testing of a non-linear Leslie model applied to a small mammal population

    International Nuclear Information System (INIS)

    Monte, Luigi

    2013-01-01

    The present work describes the application of a non-linear Leslie model for predicting the effects of ionising radiation on wild populations. The model assumes that, for protracted chronic irradiation, the effect-dose relationship is linear. In particular, the effects of radiation are modelled by relating the increase in the mortality rates of the individuals to the dose rates through a proportionality factor C. The model was tested using independent data and information from a series of experiments that were aimed at assessing the response to radiation of wild populations of meadow voles and whose results were described in the international literature. The comparison of the model results with the data selected from the above mentioned experiments showed that the model overestimated the detrimental effects of radiation on the size of irradiated populations when the values of C were within the range derived from the median lethal dose (L 50 ) for small mammals. The described non-linear model suggests that the non-expressed biotic potential of the species whose growth is limited by processes of environmental resistance, such as the competition among the individuals of the same or of different species for the exploitation of the available resources, can be a factor that determines a more effective response of population to the radiation effects. -- Highlights: • A model to assess the radiation effects on wild population is described. • The model is based on non-linear Leslie matrix. • The model is applied to small mammals living in an irradiated meadow. • Model output is conservative if effect-dose factor estimated from L 50 is used. • Systemic response to stress of populations in competitive conditions may be more effective

  19. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

    Directory of Open Access Journals (Sweden)

    Meghann K. Devlin-Durante

    2017-11-01

    Full Text Available The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  20. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata.

    Science.gov (United States)

    Devlin-Durante, Meghann K; Baums, Iliana B

    2017-01-01

    The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata , to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  1. Construction and analysis of a giant gartersnake (Thamnophis gigas) population projection model

    Science.gov (United States)

    Rose, Jonathan P.; Ersan, Julia S. M.; Wylie, Glenn D.; Casazza, Michael L.; Halstead, Brian J.

    2018-03-19

    The giant gartersnake (Thamnophis gigas) is a state and federally threatened species precinctive to California. The range of the giant gartersnake has contracted in the last century because its wetland habitat has been drained for agriculture and development. As a result of this habitat alteration, giant gartersnakes now largely persist in and near rice agriculture in the Sacramento Valley, because the system of canals that conveys water for rice growing approximates historical wetland habitat. Many aspects of the demography of giant gartersnakes are unknown, including how individuals grow throughout their life, how size influences reproduction, and how survival varies over time and among populations. We studied giant gartersnakes throughout the Sacramento Valley of California from 1995 to 2016 using capture-mark-recapture to study the growth, reproduction, and survival of this threatened species. We then use these data to construct an Integral Projection Model, and analyze this demographic model to understand which vital rates contribute most to the growth rate of giant gartersnake populations. We find that giant gartersnakes exhibit indeterminate growth; growth slows as individuals’ age. Fecundity, probability of reproduction, and survival all increase with size, although survival may decline for the largest female giant gartersnakes. The population growth rate of giant gartersnakes is most influenced by the survival and growth of large adult females, and the size at which 1 year old recruits enter the population. Our results indicate that management actions benefitting these influential demographic parameters will have the greatest positive effect on giant gartersnake population growth rates, and therefore population persistence. This study informs the conservation and management of giant gartersnakes and their habitat, and illustrates the effectiveness of hierarchical Bayesian models for the study of rare and elusive species.

  2. Evaluation of Aerosol Mixing State Classes in the GISS Modele-matrix Climate Model Using Single-particle Mass Spectrometry Measurements

    Science.gov (United States)

    Bauer, Susanne E.; Ault, Andrew; Prather, Kimberly A.

    2013-01-01

    Aerosol particles in the atmosphere are composed of multiple chemical species. The aerosol mixing state, which describes how chemical species are mixed at the single-particle level, provides critical information on microphysical characteristics that determine the interaction of aerosols with the climate system. The evaluation of mixing state has become the next challenge. This study uses aerosol time-of-flight mass spectrometry (ATOFMS) data and compares the results to those of the Goddard Institute for Space Studies modelE-MATRIX (Multiconfiguration Aerosol TRacker of mIXing state) model, a global climate model that includes a detailed aerosol microphysical scheme. We use data from field campaigns that examine a variety of air mass regimens (urban, rural, and maritime). At all locations, polluted areas in California (Riverside, La Jolla, and Long Beach), a remote location in the Sierra Nevada Mountains (Sugar Pine) and observations from Jeju (South Korea), the majority of aerosol species are internally mixed. Coarse aerosol particles, those above 1 micron, are typically aged, such as coated dust or reacted sea-salt particles. Particles below 1 micron contain large fractions of organic material, internally-mixed with sulfate and black carbon, and few external mixtures. We conclude that observations taken over multiple weeks characterize typical air mass types at a given location well; however, due to the instrumentation, we could not evaluate mass budgets. These results represent the first detailed comparison of single-particle mixing states in a global climate model with real-time single-particle mass spectrometry data, an important step in improving the representation of mixing state in global climate models.

  3. Modeling disturbance-based native invasive species control and its implications for management.

    Science.gov (United States)

    Shackelford, Nancy; Renton, Michael; Perring, Michael P; Hobbs, Richard J

    2013-09-01

    Shifts in disturbance regime have often been linked to invasion in systems by native and nonnative species. This process can have negative effects on biodiversity and ecosystem function. Degradation may be ameliorated by the reinstatement of the disturbance regimes, such as the reintroduction of fire in pyrogenic systems. Modeling is one method through which potential outcomes of different regimes can be investigated. We created a population model to examine the control of a native invasive that is expanding and increasing in abundance due to suppressed fire. Our model, parameterized with field data from a case study of the tree Allocasuarina huegeliana in Australian sandplain heath, simulated different fire return intervals with and without the additional management effort of mechanical removal of the native invader. Population behavior under the different management options was assessed, and general estimates of potential biodiversity impacts were compared. We found that changes in fire return intervals made no significant difference in the increase and spread of the population. However, decreased fire return intervals did lower densities reached in the simulated heath patch as well as the estimated maximum biodiversity impacts. When simulating both mechanical removal and fire, we found that the effects of removal depended on the return intervals and the strategy used. Increase rates were not significantly affected by any removal strategy. However, we found that removal, particularly over the whole patch rather than focusing on satellite populations, could decrease average and maximum densities reached and thus decrease the predicted biodiversity impacts. Our simulation model shows that disturbance-based management has the potential to control native invasion in cases where shifted disturbance is the likely driver of the invasion. The increased knowledge gained through the modeling methods outlined can inform management decisions in fire regime planning that

  4. Integrated analysis for population estimation, management impact evaluation, and decision-making for a declining species

    Science.gov (United States)

    Crawford, Brian A.; Moore, Clinton; Norton, Terry M.; Maerz, John C.

    2018-01-01

    A challenge for making conservation decisions is predicting how wildlife populations respond to multiple, concurrent threats and potential management strategies, usually under substantial uncertainty. Integrated modeling approaches can improve estimation of demographic rates necessary for making predictions, even for rare or cryptic species with sparse data, but their use in management applications is limited. We developed integrated models for a population of diamondback terrapins (Malaclemys terrapin) impacted by road-associated threats to (i) jointly estimate demographic rates from two mark-recapture datasets, while directly estimating road mortality and the impact of management actions deployed during the study; and (ii) project the population using population viability analysis under simulated management strategies to inform decision-making. Without management, population extirpation was nearly certain due to demographic impacts of road mortality, predators, and vegetation. Installation of novel flashing signage increased survival of terrapins that crossed roads by 30%. Signage, along with small roadside barriers installed during the study, increased population persistence probability, but the population was still predicted to decline. Management strategies that included actions targeting multiple threats and demographic rates resulted in the highest persistence probability, and roadside barriers, which increased adult survival, were predicted to increase persistence more than other actions. Our results support earlier findings showing mitigation of multiple threats is likely required to increase the viability of declining populations. Our approach illustrates how integrated models may be adapted to use limited data efficiently, represent system complexity, evaluate impacts of threats and management actions, and provide decision-relevant information for conservation of at-risk populations.

  5. Dynamic analysis of a parasite population model

    Science.gov (United States)

    Sibona, G. J.; Condat, C. A.

    2002-03-01

    We study the dynamics of a model that describes the competitive interaction between an invading species (a parasite) and its antibodies in an living being. This model was recently used to examine the dynamical competition between Tripanosoma cruzi and its antibodies during the acute phase of Chagas' disease. Depending on the antibody properties, the model yields three types of outcomes, corresponding, respectively, to healing, chronic disease, and host death. Here, we study the dynamics of the parasite-antibody interaction with the help of simulations, obtaining phase trajectories and phase diagrams for the system. We show that, under certain conditions, the size of the parasite inoculation can be crucial for the infection outcome and that a retardation in the stimulated production of an antibody species may result in the parasite gaining a definitive advantage. We also find a criterion for the relative sizes of the parameters that are required if parasite-generated decoys are indeed to help the invasion. Decoys may also induce a qualitatively different outcome: a limit cycle for the antibody-parasite population phase trajectories.

  6. Modelling multi-pulse population dynamics from ultrafast spectroscopy.

    Directory of Open Access Journals (Sweden)

    Luuk J G W van Wilderen

    2011-03-01

    Full Text Available Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio- physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox that describes the finite bleach (orientation effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective excitation (photoselection and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical

  7. Modelling multi-pulse population dynamics from ultrafast spectroscopy.

    Science.gov (United States)

    van Wilderen, Luuk J G W; Lincoln, Craig N; van Thor, Jasper J

    2011-03-21

    Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is

  8. How to conserve threatened Chinese plant species with extremely small populations?

    Directory of Open Access Journals (Sweden)

    Sergei Volis

    2016-02-01

    Full Text Available The Chinese flora occupies a unique position in global plant diversity, but is severely threatened. Although biodiversity conservation in China has made significant progress over the past decades, many wild plant species have extremely small population sizes and therefore are in extreme danger of extinction. The concept of plant species with extremely small populations (PSESPs, recently adopted and widely accepted in China, lacks a detailed description of the methodology appropriate for conserving PSESPs. Strategies for seed sampling, reintroduction, protecting PSESP locations, managing interactions with the local human population, and other conservation aspects can substantially differ from those commonly applied to non-PSESPs. The present review is an attempt to provide a detailed conservation methodology with realistic and easy-to-follow guidelines for PSESPs in China.

  9. MILES extended : Stellar population synthesis models from the optical to the infrared

    NARCIS (Netherlands)

    Rock, B.; Vazdekis, A.; Ricciardelli, E.; Peletier, R. F.; Knapen, J. H.; Falcon-Barroso, J.

    We present the first single-burst stellar population models, which covers the optical and the infrared wavelength range between 3500 and 50 000 angstrom and which are exclusively based on empirical stellar spectra. To obtain these joint models, we combined the extended MILES models in the optical

  10. Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae

    Directory of Open Access Journals (Sweden)

    Félix Marie-Anne

    2012-06-01

    Full Text Available Abstract Background The nematode Caenorhabditis elegans is a major model organism in laboratory biology. Very little is known, however, about its ecology, including where it proliferates. In the past, C. elegans was mainly isolated from human-made compost heaps, where it was overwhelmingly found in the non-feeding dauer diapause stage. Results C. elegans and C. briggsae were found in large, proliferating populations in rotting plant material (fruits and stems in several locations in mainland France. Both species were found to co-occur in samples isolated from a given plant species. Population counts spanned a range from one to more than 10,000 Caenorhabditis individuals on a single fruit or stem. Some populations with an intermediate census size (10 to 1,000 contained no dauer larvae at all, whereas larger populations always included some larvae in the pre-dauer or dauer stages. We report on associated micro-organisms, including pathogens. We systematically sampled a spatio-temporally structured set of rotting apples in an apple orchard in Orsay over four years. C. elegans and C. briggsae were abundantly found every year, but their temporal distributions did not coincide. C. briggsae was found alone in summer, whereas both species co-occurred in early fall and C. elegans was found alone in late fall. Competition experiments in the laboratory at different temperatures show that C. briggsae out-competes C. elegans at high temperatures, whereas C. elegans out-competes C. briggsae at lower temperatures. Conclusions C. elegans and C. briggsae proliferate in the same rotting vegetal substrates. In contrast to previous surveys of populations in compost heaps, we found fully proliferating populations with no dauer larvae. The temporal sharing of the habitat by the two species coincides with their temperature preference in the laboratory, with C. briggsae populations growing faster than C. elegans at higher temperatures, and vice at lower temperatures.

  11. On reducibility and ergodicity of population projection matrix models

    DEFF Research Database (Denmark)

    Stott, Iain; Townley, Stuart; Carslake, David

    2010-01-01

    from all stages to all other stages) and therefore ergodic (whatever initial stage structure is used in the population projection, it will always exhibit the same stable asymptotic growth rate). 2. Evaluation of 652 PPM models for 171 species from the literature suggests that 24·7% of PPM models...... structure used in the population projection). In our sample of published PPMs, 15·6% are non-ergodic. 3. This presents a problem: reducible–ergodic models often defy biological rationale in their description of the life cycle but may or may not prove problematic for analysis as they often behave similarly...... of reducibility in published PPMs, with significant implications for the predictive power of such models in many cases. We suggest that as a general rule, reducibility of PPM models should be avoided. However, we provide a guide to the pertinent analysis of reducible matrix models, largely based upon whether...

  12. Optimized O'Neill/Glaser Model for Human Population of Space and its Impact on Survival Probabilities

    Science.gov (United States)

    Curreri, Peter A.

    2010-01-01

    Two contemporary issues foretell a shift from our historical Earth based industrial economy and habitation to a solar system based society. The first is the limits to Earth s carrying capacity, that is the maximum number of people that the Earth can support before a catastrophic impact to the health of the planet and human species occurs. The simple example of carrying capacity is that of a bacterial colony in a Petri dish with a limited amount of nutrient. The colony experiences exponential population growth until the carrying capacity is reached after which catastrophic depopulation often results. Estimates of the Earth s carrying capacity vary between 14 and 40 billion people. Although at current population growth rates we may have over a century before we reach Earth s carrying limit our influence on climate and resources on the planetary scale is becoming scientifically established. The second issue is the exponential growth of knowledge and technological power. The exponential growth of technology interacts with the exponential growth of population in a manner that is unique to a highly intelligent species. Thus, the predicted consequences (world famines etc.) of the limits to growth have been largely avoided due to technological advances. However, at the mid twentieth century a critical coincidence occurred in these two trends humanity obtained the technological ability to extinguish life on the planetary scale (by nuclear, chemical, biological means) and attained the ability to expand human life beyond Earth. This paper examines an optimized O'Neill/Glaser model (O Neill 1975; Curreri 2007; Detweiler and Curreri 2008) for the economic human population of space. Critical to this model is the utilization of extraterrestrial resources, solar power and spaced based labor. A simple statistical analysis is then performed which predicts the robustness of a single planet based technological society versus that of multiple world (independent habitats) society.

  13. Microsatellite DNA analysis of northern pike ( Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

    DEFF Research Database (Denmark)

    Jacobsen, B. H.; Hansen, Michael Møller; Loeschcke, V.

    2005-01-01

    The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current...... low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations...... was high (overall theta(ST) = 0.51; overall rho(ST) = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American...

  14. Extinction threshold of a population in spatial and stochastic model

    OpenAIRE

    Soroka, Yevheniia; Rublyov, Bogdan

    2016-01-01

    In this study, spatial stochastic and logistic model (SSLM) describing dynamics of a population of a certain species was analysed. The behaviour of the extinction threshold as a function of model parameters was studied. More specifically, we studied how the critical values for the model parameters that separate the cases of extinction and persistence depend on the spatial scales of the competition and dispersal kernels. We compared the simulations and analytical results to examine if and how ...

  15. The effects of spatial and temporal heterogeneity on the population dynamics of four animal species in a Danish landscape

    Directory of Open Access Journals (Sweden)

    Forchhammer Mads C

    2009-06-01

    Full Text Available Abstract Background Variation in carrying capacity and population return rates is generally ignored in traditional studies of population dynamics. Variation is hard to study in the field because of difficulties controlling the environment in order to obtain statistical replicates, and because of the scale and expense of experimenting on populations. There may also be ethical issues. To circumvent these problems we used detailed simulations of the simultaneous behaviours of interacting animals in an accurate facsimile of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of skylarks Alauda arvensis, voles Microtus agrestis, a ground beetle Bembidion lampros and a linyphiid spider Erigone atra. This allows us to quantify and evaluate the importance of spatial and temporal heterogeneity on the population dynamics of the four species. Results Both spatial and temporal heterogeneity affected the relationship between population growth rate and population density in all four species. Spatial heterogeneity accounted for 23–30% of the variance in population growth rate after accounting for the effects of density, reflecting big differences in local carrying capacity associated with the landscape features important to individual species. Temporal heterogeneity accounted for 3–13% of the variance in vole, skylark and spider, but 43% in beetles. The associated temporal variation in carrying capacity would be problematic in traditional analyses of density dependence. Return rates were less than one in all species and essentially invariant in skylarks, spiders and beetles. Return rates varied over the landscape in voles, being slower where there were larger fluctuations in local population sizes. Conclusion Our analyses estimated the traditional parameters of carrying capacities and return rates, but these are now seen as varying continuously over the landscape depending on habitat quality and the mechanisms

  16. Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii.

    Science.gov (United States)

    McAllister, Christine A; Miller, Allison J

    2016-07-01

    Autopolyploidy, genome duplication within a single lineage, can result in multiple cytotypes within a species. Geographic distributions of cytotypes may reflect the evolutionary history of autopolyploid formation and subsequent population dynamics including stochastic (drift) and deterministic (differential selection among cytotypes) processes. Here, we used a population genomic approach to investigate whether autopolyploidy occurred once or multiple times in Andropogon gerardii, a widespread, North American grass with two predominant cytotypes. Genotyping by sequencing was used to identify single nucleotide polymorphisms (SNPs) in individuals collected from across the geographic range of A. gerardii. Two independent approaches to SNP calling were used: the reference-free UNEAK pipeline and a reference-guided approach based on the sequenced Sorghum bicolor genome. SNPs generated using these pipelines were analyzed independently with genetic distance and clustering. Analyses of the two SNP data sets showed very similar patterns of population-level clustering of A. gerardii individuals: a cluster of A. gerardii individuals from the southern Plains, a northern Plains cluster, and a western cluster. Groupings of individuals corresponded to geographic localities regardless of cytotype: 6x and 9x individuals from the same geographic area clustered together. SNPs generated using reference-guided and reference-free pipelines in A. gerardii yielded unique subsets of genomic data. Both data sets suggest that the 9x cytotype in A. gerardii likely evolved multiple times from 6x progenitors across the range of the species. Genomic approaches like GBS and diverse bioinformatics pipelines used here facilitate evolutionary analyses of complex systems with multiple ploidy levels. © 2016 Botanical Society of America.

  17. Single generation cycles and delayed feedback cycles are not separate phenomena.

    Science.gov (United States)

    Pfaff, T; Brechtel, A; Drossel, B; Guill, C

    2014-12-01

    We study a simple model for generation cycles, which are oscillations with a period of one or a few generation times of the species. The model is formulated in terms of a single delay-differential equation for the population density of an adult stage, with recruitment to the adult stage depending on the intensity of competition during the juvenile phase. This model is a simplified version of a group of models proposed by Gurney and Nisbet, who were the first to distinguish between single-generation cycles and delayed-feedback cycles. According to these authors, the two oscillation types are caused by different mechanisms and have periods in different intervals, which are one to two generation times for single-generation cycles and two to four generation times for delayed-feedback cycles. By abolishing the strict coupling between the maturation time and the time delay between competition and its effect on the population dynamics, we find that single-generation cycles and delayed-feedback cycles occur in the same model version, with a gradual transition between the two as the model parameters are varied over a sufficiently large range. Furthermore, cycle periods are not bounded to lie within single octaves. This implies that a clear distinction between different types of generation cycles is not possible. Cycles of all periods and even chaos can be generated by varying the parameters that determine the time during which individuals from different cohorts compete with each other. This suggests that life-cycle features in the juvenile stage and during the transition to the adult stage are important determinants of the dynamics of density limited populations. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. POPULATION SYNCHRONY WITHIN AND AMONG LEPIDOPTERA SPECIES IN RELATION TO WEATHER, PHYLOGENY, AND LARVEL PHENOLOGY

    Science.gov (United States)

    1. The population dynamics of native herbivore species in central Appalachian deciduous forests were studied by analysing patterns of synchrony among intra- and interspecific populations and weather. 2. Spatial synchrony of 10 Lepidoptera species and three weather variables (min...

  19. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Science.gov (United States)

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  20. Competition between the sperm of a single male can increase the evolutionary rate of haploid expressed genes.

    Science.gov (United States)

    Ezawa, Kiyoshi; Innan, Hideki

    2013-07-01

    The population genetic behavior of mutations in sperm genes is theoretically investigated. We modeled the processes at two levels. One is the standard population genetic process, in which the population allele frequencies change generation by generation, depending on the difference in selective advantages. The other is the sperm competition during each genetic transmission from one generation to the next generation. For the sperm competition process, we formulate the situation where a huge number of sperm with alleles A and B, produced by a single heterozygous male, compete to fertilize a single egg. This "minimal model" demonstrates that a very slight difference in sperm performance amounts to quite a large difference between the alleles' winning probabilities. By incorporating this effect of paternity-sharing sperm competition into the standard population genetic process, we show that fierce sperm competition can enhance the fixation probability of a mutation with a very small phenotypic effect at the single-sperm level, suggesting a contribution of sperm competition to rapid amino acid substitutions in haploid-expressed sperm genes. Considering recent genome-wide demonstrations that a substantial fraction of the mammalian sperm genes are haploid expressed, our model could provide a potential explanation of rapid evolution of sperm genes with a wide variety of functions (as long as they are expressed in the haploid phase). Another advantage of our model is that it is applicable to a wide range of species, irrespective of whether the species is externally fertilizing, polygamous, or monogamous. The theoretical result was applied to mammalian data to estimate the selection intensity on nonsynonymous mutations in sperm genes.

  1. Genetic Differentiations among the Populations of Salvia japonica (Lamiaceae and Its Related Species

    Directory of Open Access Journals (Sweden)

    SUDARMONO

    2008-03-01

    Full Text Available Morphological and genetic variations within Salvia japonica (Lamiaceae and its related species in Japan were analyzed for clarifying their taxonomic significance. The genetic variations were explored through chloroplast and nuclear ribosomal DNA sequences and allozyme polymorphisms. Since chromosome numbers characterized the genus of Salvia, we also examined whether the karyotypes were different. We examined 58 populations of S. japonica and 14 populations of others species of Salvia. Among the populations of S. japonica represented four forms (f. japonica, f. longipes, f. lanuginosa and f. albiflora. The size of chromosomes were various among Salvia spp. Based on the allozyme as well as the DNA sequence, the populations of S. japonica separated from the others Salvia species. The populations of S. japonica exhibited four combinations of the morphological characters. However, these combinations did not correlate to the four forms of S. japonica. In addition, the morphological variations did not correlate to the allozyme and DNA sequences. It is suggested that the four morphological variations as well as the four form of S. japonica should not considered to be a taxonomic unit; accordingly, S. japonica were considered to be still at the early stage of speciation process.

  2. Impacts of land cover data selection and trait parameterisation on dynamic modelling of species' range expansion.

    Directory of Open Access Journals (Sweden)

    Risto K Heikkinen

    Full Text Available Dynamic models for range expansion provide a promising tool for assessing species' capacity to respond to climate change by shifting their ranges to new areas. However, these models include a number of uncertainties which may affect how successfully they can be applied to climate change oriented conservation planning. We used RangeShifter, a novel dynamic and individual-based modelling platform, to study two potential sources of such uncertainties: the selection of land cover data and the parameterization of key life-history traits. As an example, we modelled the range expansion dynamics of two butterfly species, one habitat specialist (Maniola jurtina and one generalist (Issoria lathonia. Our results show that projections of total population size, number of occupied grid cells and the mean maximal latitudinal range shift were all clearly dependent on the choice made between using CORINE land cover data vs. using more detailed grassland data from three alternative national databases. Range expansion was also sensitive to the parameterization of the four considered life-history traits (magnitude and probability of long-distance dispersal events, population growth rate and carrying capacity, with carrying capacity and magnitude of long-distance dispersal showing the strongest effect. Our results highlight the sensitivity of dynamic species population models to the selection of existing land cover data and to uncertainty in the model parameters and indicate that these need to be carefully evaluated before the models are applied to conservation planning.

  3. Model of yield response of corn to plant population and absorption of solar energy.

    Directory of Open Access Journals (Sweden)

    Allen R Overman

    Full Text Available Biomass yield of agronomic crops is influenced by a number of factors, including crop species, soil type, applied nutrients, water availability, and plant population. This article is focused on dependence of biomass yield (Mg ha(-1 and g plant(-1 on plant population (plants m(-2. Analysis includes data from the literature for three independent studies with the warm-season annual corn (Zea mays L. grown in the United States. Data are analyzed with a simple exponential mathematical model which contains two parameters, viz. Y(m (Mg ha(-1 for maximum yield at high plant population and c (m(2 plant(-1 for the population response coefficient. This analysis leads to a new parameter called characteristic plant population, x(c = 1/c (plants m(-2. The model is shown to describe the data rather well for the three field studies. In one study measurements were made of solar radiation at different positions in the plant canopy. The coefficient of absorption of solar energy was assumed to be the same as c and provided a physical basis for the exponential model. The three studies showed no definitive peak in yield with plant population, but generally exhibited asymptotic approach to maximum yield with increased plant population. Values of x(c were very similar for the three field studies with the same crop species.

  4. Individualistic population responses of five frog species in two changing tropical environments over time.

    Directory of Open Access Journals (Sweden)

    Mason J Ryan

    Full Text Available Roughly 40% of amphibian species are in decline with habitat loss, disease, and climate change being the most cited threats. Heterogeneity of extrinsic (e.g. climate and intrinsic (e.g. local adaptations factors across a species' range should influence population response to climate change and other threats. Here we examine relative detectability changes for five direct-developing leaf litter frogs between 42-year sampling periods at one Lowland Tropical Forest site (51 m.a.s.l. and one Premontane Wet Forest site (1100 m.a.s.l. in southwest Costa Rica. We identify individualistic changes in relative detectability among populations between sampling periods at different elevations. Both common and rare species showed site-specific declines, and no species exhibited significant declines at both sites. Detection changes are correlated with changes in temperature, dry season rainfall, and leaf litter depth since 1969. Our study species share Least Concern conservation status, life history traits, and close phylogenetic relationship, yet their populations changed individualistically both within and among species. These results counter current views of the uniformity or predictability of amphibian decline response and suggest additional complexity for conservation decisions.

  5. Can a Single Amphibian Species Be a Good Biodiversity Indicator?

    Directory of Open Access Journals (Sweden)

    David Sewell

    2009-11-01

    Full Text Available Although amphibians have been widely promoted as indicators of biodiversity and environmental change, rigorous tests are lacking. Here key indicator criteria are distilled from published papers, and a species that has been promoted as a bioindicator, the great crested newt, is tested against them. Although a link was established between the presence of great crested newts and aquatic plant diversity, this was not repeated with the diversity of macroinvertebrates. Equally, amphibians do not meet many of the published criteria of bioindicators. Our research suggests that a suite of indicators, rather than a single species, will usually be required.

  6. On population size estimators in the Poisson mixture model.

    Science.gov (United States)

    Mao, Chang Xuan; Yang, Nan; Zhong, Jinhua

    2013-09-01

    Estimating population sizes via capture-recapture experiments has enormous applications. The Poisson mixture model can be adopted for those applications with a single list in which individuals appear one or more times. We compare several nonparametric estimators, including the Chao estimator, the Zelterman estimator, two jackknife estimators and the bootstrap estimator. The target parameter of the Chao estimator is a lower bound of the population size. Those of the other four estimators are not lower bounds, and they may produce lower confidence limits for the population size with poor coverage probabilities. A simulation study is reported and two examples are investigated. © 2013, The International Biometric Society.

  7. Multiple Phytophthora species associated with a single riparian ecosystem in South Africa.

    Science.gov (United States)

    Nagel, Jan H; Slippers, Bernard; Wingfield, Michael J; Gryzenhout, Marieka

    2015-01-01

    The diversity of Phytophthora spp. in rivers and riparian ecosystems has received considerable international attention, although little such research has been conducted in South Africa. This study determined the diversity of Phytophthora spp. within a single river in Gauteng province of South Africa. Samples were collected over 1 y including biweekly river baiting with Rhododendron indicum leaves. Phytophthora isolates were identified with phylogenetic analyses of sequences for the internal transcribed spacer (ITS) region of the ribosomal DNA and the mitochondrial cytochrome oxidase c subunit I (coxI) gene. Eight Phytophthora spp. were identified, including a new taxon, P. taxon Sisulu-river, and two hybrid species from Cooke's ITS clade 6. Of these, species from Clade 6 were the most abundant, including P. chlamydospora and P. lacustris. Species residing in Clade 2 also were encountered, including P. multivora, P. plurivora and P. citrophthora. The detection of eight species in this investigation of Phytophthora diversity in a single riparian river ecosystem in northern South Africa adds to the known diversity of this genus in South Africa and globally. © 2015 by The Mycological Society of America.

  8. Discrete time population dynamics of a two-stage species with recruitment and capture

    International Nuclear Information System (INIS)

    Ladino, Lilia M.; Mammana, Cristiana; Michetti, Elisabetta; Valverde, Jose C.

    2016-01-01

    This work models and analyzes the dynamics of a two-stage species with recruitment and capture factors. It arises from the discretization of a previous model developed by Ladino and Valverde (2013), which represents a progress in the knowledge of the dynamics of exploited populations. Although the methods used here are related to the study of discrete-time systems and are different from those related to continuous version, the results are similar in both the discrete and the continuous case what confirm the skill in the selection of the factors to design the model. Unlike for the continuous-time case, for the discrete-time one some (non-negative) parametric constraints are derived from the biological significance of the model and become fundamental for the proofs of such results. Finally, numerical simulations show different scenarios of dynamics related to the analytical results which confirm the validity of the model.

  9. Population Pharmacokinetic Modelling of FE 999049, a Recombinant Human Follicle-Stimulating Hormone, in Healthy Women After Single Ascending Doses

    DEFF Research Database (Denmark)

    Rose, Trine Høyer; Röshammar, Daniel; Erichsen, Lars

    2016-01-01

    reproductive technologies. Methods: Serum FSH levels were measured following a single subcutaneous FE 999049 injection of 37.5, 75, 150, 225 or 450 IU in 27 pituitary-suppressed healthy female subjects participating in this first-in-human single ascending dose trial. Data was analysed by nonlinear mixed...... volume of distribution (V/F) estimates were found to increase with body weight. Body weight was included as an allometrically scaled covariate with a power exponent of 0.75 for CL/F and 1 for V/F. Conclusions: The single-dose pharmacokinetics of FE 999049 were adequately described by a population...

  10. Parallel and costly changes to cellular immunity underlie the evolution of parasitoid resistance in three Drosophila species.

    Directory of Open Access Journals (Sweden)

    John E McGonigle

    2017-10-01

    Full Text Available A priority for biomedical research is to understand the causes of variation in susceptibility to infection. To investigate genetic variation in a model system, we used flies collected from single populations of three different species of Drosophila and artificially selected them for resistance to the parasitoid wasp Leptopilina boulardi, and found that survival rates increased 3 to 30 fold within 6 generations. Resistance in all three species involves a large increase in the number of the circulating hemocytes that kill parasitoids. However, the different species achieve this in different ways, with D. melanogaster moving sessile hemocytes into circulation while the other species simply produce more cells. Therefore, the convergent evolution of the immune phenotype has different developmental bases. These changes are costly, as resistant populations of all three species had greatly reduced larval survival. In all three species resistance is only costly when food is in short supply, and resistance was rapidly lost from D. melanogaster populations when food is restricted. Furthermore, evolving resistance to L. boulardi resulted in cross-resistance against other parasitoids. Therefore, whether a population evolves resistance will depend on ecological conditions including food availability and the presence of different parasite species.

  11. Moving across the border: Modeling migratory bat populations

    Science.gov (United States)

    Ruscena, Wiederholt; López-Hoffman, Laura; Cline, Jon; Medellin, Rodrigo; Cryan, Paul M.; Russell, Amy; McCracken, Gary; Diffendorfer, Jay; Semmens, Darius J.

    2013-01-01

    The migration of animals across long distances and between multiple habitats presents a major challenge for conservation. For the migratory Mexican free-tailed bat (Tadarida brasiliensis mexicana), these challenges include identifying and protecting migratory routes and critical roosts in two countries, the United States and Mexico. Knowledge and conservation of bat migratory routes is critical in the face of increasing threats from climate change and wind turbines that might decrease migratory survival. We employ a new modeling approach for bat migration, network modeling, to simulate migratory routes between winter habitat in southern Mexico and summer breeding habitat in northern Mexico and the southwestern United States. We use the model to identify key migratory routes and the roosts of greatest conservation value to the overall population. We measure roost importance by the degree to which the overall bat population declined when the roost was removed from the model. The major migratory routes—those with the greatest number of migrants—were between winter habitat in southern Mexico and summer breeding roosts in Texas and the northern Mexican states of Sonora and Nuevo Leon. The summer breeding roosts in Texas, Sonora, and Nuevo Leon were the most important for maintaining population numbers and network structure – these are also the largest roosts. This modeling approach contributes to conservation efforts by identifying the most influential areas for bat populations, and can be used as a tool to improve our understanding of bat migration for other species. We anticipate this approach will help direct coordination of habitat protection across borders.

  12. Population Viability of Avian Endangered Species: the PVAvES Program

    National Research Council Canada - National Science Library

    Melton, Robert

    2001-01-01

    .... The program is designed to assess the viability of endangered bird species populations on U.S. Army lands. It also facilitates the comparison of alternative ecological scenarios based on different assumptions about the effects of natural or human...

  13. Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species.

    Science.gov (United States)

    Prunier, Rachel; Akman, Melis; Kremer, Colin T; Aitken, Nicola; Chuah, Aaron; Borevitz, Justin; Holsinger, Kent E

    2017-05-01

    The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian F ST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species. © 2017 Prunier et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY-NC).

  14. Disjunct populations of European vascular plant species keep the same climatic niches

    DEFF Research Database (Denmark)

    Wasof, Safaa; Lenoir, Jonathan; Aarrestad, Per Arild

    2015-01-01

    separated for thousands of years. Location: European Alps and Fennoscandia. Methods: Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly......Aim: Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been...... to be largely valid for arctic-alpine plants....

  15. Temporal variation in population size of European bird species: effects of latitude and marginality of distribution.

    Directory of Open Access Journals (Sweden)

    José J Cuervo

    Full Text Available In the Northern Hemisphere, global warming has been shown to affect animal populations in different ways, with southern populations in general suffering more from increased temperatures than northern populations of the same species. However, southern populations are also often marginal populations relative to the entire breeding range, and marginality may also have negative effects on populations. To disentangle the effects of latitude (possibly due to global warming and marginality on temporal variation in population size, we investigated European breeding bird species across a latitudinal gradient. Population size estimates were regressed on years, and from these regressions we obtained the slope (a proxy for population trend and the standard error of the estimate (SEE (a proxy for population fluctuations. The possible relationships between marginality or latitude on one hand and slopes or SEE on the other were tested among populations within species. Potentially confounding factors such as census method, sampling effort, density-dependence, habitat fragmentation and number of sampling years were controlled statistically. Population latitude was positively related to regression slopes independent of marginality, with more positive slopes (i.e., trends in northern than in southern populations. The degree of marginality was positively related to SEE independent of latitude, with marginal populations showing larger SEE (i.e., fluctuations than central ones. Regression slopes were also significantly related to our estimate of density-dependence and SEE was significantly affected by the census method. These results are consistent with a scenario in which southern and northern populations of European bird species are negatively affected by marginality, with southern populations benefitting less from global warming than northern populations, thus potentially making southern populations more vulnerable to extinction.

  16. Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species.

    Science.gov (United States)

    Yan, Yu-Bin; Duke, Norm C; Sun, Mei

    2016-01-01

    Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata , and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa , suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

  17. A single ectomycorrhizal fungal species can enable a Pinus invasion.

    Science.gov (United States)

    Hayward, Jeremy; Horton, Thomas R; Pauchard, Aníbal; Nuñnez, Martin A

    2015-05-01

    Like all obligately ectomycorrhizal plants, pines require ectomycorrhizal fungal symbionts to complete their life cycle. Pines introduced into regions far from their native range are typically incompatible with local ectomycorrhizal fungi, and, when they invade, coinvade with fungi from their native range. While the identities and distributions of coinvasive fungal symbionts of pine invasions are poorly known, communities that have been studied are notably depauperate. However, it is not yet clear whether any number of fungal coinvaders is able to support a Pinaceae invasion, or whether very depauperate communities are unable to invade. Here, we ask whether there is evidence for a minimum species richness of fungal symbionts necessary to support a pine/ectomycorrhizal fungus coinvasion. We sampled a Pinus contorta invasion front near Coyhaique, Chile, using molecular barcoding to identify ectomycorrhizal fungi. We report that the site has a total richness of four species, and that many invasive trees appear to be supported by only a single ectomycorrhizal fungus, Suillus luteus. We conclude that a single ectomycorrhizal (ECM) fungus can suffice to enable a pine invasion.

  18. Delay-induced wave instabilities in single-species reaction-diffusion systems

    Science.gov (United States)

    Otto, Andereas; Wang, Jian; Radons, Günter

    2017-11-01

    The Turing (wave) instability is only possible in reaction-diffusion systems with more than one (two) components. Motivated by the fact that a time delay increases the dimension of a system, we investigate the presence of diffusion-driven instabilities in single-species reaction-diffusion systems with delay. The stability of arbitrary one-component systems with a single discrete delay, with distributed delay, or with a variable delay is systematically analyzed. We show that a wave instability can appear from an equilibrium of single-species reaction-diffusion systems with fluctuating or distributed delay, which is not possible in similar systems with constant discrete delay or without delay. More precisely, we show by basic analytic arguments and by numerical simulations that fast asymmetric delay fluctuations or asymmetrically distributed delays can lead to wave instabilities in these systems. Examples, for the resulting traveling waves are shown for a Fisher-KPP equation with distributed delay in the reaction term. In addition, we have studied diffusion-induced instabilities from homogeneous periodic orbits in the same systems with variable delay, where the homogeneous periodic orbits are attracting resonant periodic solutions of the system without diffusion, i.e., periodic orbits of the Hutchinson equation with time-varying delay. If diffusion is introduced, standing waves can emerge whose temporal period is equal to the period of the variable delay.

  19. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline

    2017-02-15

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  20. Stochastic resonance in a generalized Von Foerster population growth model

    Energy Technology Data Exchange (ETDEWEB)

    Lumi, N.; Mankin, R. [Institute of Mathematics and Natural Sciences, Tallinn University, 25 Narva Road, 10120 Tallinn (Estonia)

    2014-11-12

    The stochastic dynamics of a population growth model, similar to the Von Foerster model for human population, is studied. The influence of fluctuating environment on the carrying capacity is modeled as a multiplicative dichotomous noise. It is established that an interplay between nonlinearity and environmental fluctuations can cause single unidirectional discontinuous transitions of the mean population size versus the noise amplitude, i.e., an increase of noise amplitude can induce a jump from a state with a moderate number of individuals to that with a very large number, while by decreasing the noise amplitude an opposite transition cannot be effected. An analytical expression of the mean escape time for such transitions is found. Particularly, it is shown that the mean transition time exhibits a strong minimum at intermediate values of noise correlation time, i.e., the phenomenon of stochastic resonance occurs. Applications of the results in ecology are also discussed.

  1. How can model comparison help improving species distribution models?

    Directory of Open Access Journals (Sweden)

    Emmanuel Stephan Gritti

    Full Text Available Today, more than ever, robust projections of potential species range shifts are needed to anticipate and mitigate the impacts of climate change on biodiversity and ecosystem services. Such projections are so far provided almost exclusively by correlative species distribution models (correlative SDMs. However, concerns regarding the reliability of their predictive power are growing and several authors call for the development of process-based SDMs. Still, each of these methods presents strengths and weakness which have to be estimated if they are to be reliably used by decision makers. In this study we compare projections of three different SDMs (STASH, LPJ and PHENOFIT that lie in the continuum between correlative models and process-based models for the current distribution of three major European tree species, Fagussylvatica L., Quercusrobur L. and Pinussylvestris L. We compare the consistency of the model simulations using an innovative comparison map profile method, integrating local and multi-scale comparisons. The three models simulate relatively accurately the current distribution of the three species. The process-based model performs almost as well as the correlative model, although parameters of the former are not fitted to the observed species distributions. According to our simulations, species range limits are triggered, at the European scale, by establishment and survival through processes primarily related to phenology and resistance to abiotic stress rather than to growth efficiency. The accuracy of projections of the hybrid and process-based model could however be improved by integrating a more realistic representation of the species resistance to water stress for instance, advocating for pursuing efforts to understand and formulate explicitly the impact of climatic conditions and variations on these processes.

  2. Evaluation of multi-species weed competition and weeds population dynamic in corn Zea mays L. field

    Directory of Open Access Journals (Sweden)

    S Mijani

    2016-05-01

    Full Text Available In order to examine the multi-species weed competition in corn field an experiment as an interval mapping was carried out at the Agricultural Research field of Ferdowsi University of Mashhad during growing season 2009-2010. At 3-4 leafy stages of corn, 20 non-destructive quadrates determine and the density of weeds was counted separately. At the same time, 20 destructive quadrates determine and in addition of counting number of plants, leaf area index and dry weight of each species were recorded separately. By using data from previous section, hyperbolic functions were fitted. In these functions number of species serve as the independent variable, weight or leaf area was considered as the dependent variable. With the help of these functions and leaf dry weight of each species was determined for non-destructive quadrates at this stage. Relative leaf area at early season as independent variables and natural logarithm of individual plant weight at later season as dependent variable in a multiple linear regression was fitted to obtain the interspecies competition coefficients. Based on ln of weight of single plant equation the weed interference effects on the corn yield can be divided into two groups: inhibition (negative sign and stimulation (positive sign. Among all weeds, night shade (Solanum nigrum L., redroot pigweed (Amaranthus retroflexus L. and lambsquarter (Chenopodium album L. had positive effects on corn yield, respectively. In fact, these weeds had competition and negative impacts on other weeds and reduced their competition power with corn and caused facilitation role on corn yield. At the end of growing season of corn, population of lambsquarter and Common purslane (Portulaca oleracea L. decreased while population of barnyard grass(Echinochloa crus-galli L., redroot pigweed and night shade increased.

  3. Population pharmacokinetics of artesunate and dihydroartemisinin following single- and multiple-dosing of oral artesunate in healthy subjects

    Directory of Open Access Journals (Sweden)

    Kirsch Lee E

    2009-12-01

    Full Text Available Abstract Background The population pharmacokinetics of artesunate (AS and its active metabolite dihydroartemisinin (DHA were studied in healthy subjects receiving single- or multiple-dosing of AS orally either in combination with pyronaridine (PYR or as a monotherapy with or without food. Methods Data from 118 concentration-time profiles arising from 91 healthy Korean subjects were pooled from four Phase I clinical studies. Subjects received 2-5 mg/kg of single- and multiple-dosing of oral AS either in combination with PYR or as a monotherapy with or without food. Plasma AS and DHA were measured simultaneously using a validated liquid chromatography- mass spectrometric method with a lower limit of quantification of 1 ng/mL for both AS and DHA. Nonlinear mixed-effect modelling was used to obtain the pharmacokinetic and variability (inter-individual and residual variability parameter estimates. Results A novel parent-metabolite pharmacokinetic model consisting of a dosing compartment, a central compartment for AS, a central compartment and a peripheral compartment for DHA was developed. AS and DHA data were modelled simultaneously assuming stoichiometric conversion to DHA. AS was rapidly absorbed with a population estimate of absorption rate constant (Ka of 3.85 h-1. The population estimates of apparent clearance (CL/F and volume of distribution (V2/F for AS were 1190 L/h with 36.2% inter-individual variability (IIV and 1210 L with 57.4% IIV, respectively. For DHA, the population estimates of apparent clearance (CLM/F and central volume of distribution (V3/F were 93.7 L/h with 28% IIV and 97.1 L with 30% IIV, respectively. The population estimates of apparent inter-compartmental clearance (Q/F and peripheral volume of distribution (V4/F for DHA were 5.74 L/h and 18.5 L, respectively. Intake of high-fat and high-caloric meal prior to the drug administration resulted in 84% reduction in Ka. Body weight impacted CLM/F, such that a unit change in

  4. Mechanistic species distribution modelling as a link between physiology and conservation.

    Science.gov (United States)

    Evans, Tyler G; Diamond, Sarah E; Kelly, Morgan W

    2015-01-01

    Climate change conservation planning relies heavily on correlative species distribution models that estimate future areas of occupancy based on environmental conditions encountered in present-day ranges. The approach benefits from rapid assessment of vulnerability over a large number of organisms, but can have poor predictive power when transposed to novel environments and reveals little in the way of causal mechanisms that define changes in species distribution or abundance. Having conservation planning rely largely on this single approach also increases the risk of policy failure. Mechanistic models that are parameterized with physiological information are expected to be more robust when extrapolating distributions to future environmental conditions and can identify physiological processes that set range boundaries. Implementation of mechanistic species distribution models requires knowledge of how environmental change influences physiological performance, and because this information is currently restricted to a comparatively small number of well-studied organisms, use of mechanistic modelling in the context of climate change conservation is limited. In this review, we propose that the need to develop mechanistic models that incorporate physiological data presents an opportunity for physiologists to contribute more directly to climate change conservation and advance the field of conservation physiology. We begin by describing the prevalence of species distribution modelling in climate change conservation, highlighting the benefits and drawbacks of both mechanistic and correlative approaches. Next, we emphasize the need to expand mechanistic models and discuss potential metrics of physiological performance suitable for integration into mechanistic models. We conclude by summarizing other factors, such as the need to consider demography, limiting broader application of mechanistic models in climate change conservation. Ideally, modellers, physiologists and

  5. Avian malaria in Hawaiian forest birds: Infection and population impacts across species and elevations

    Science.gov (United States)

    Samuel, Michael D.; Woodworth, Bethany L.; Atkinson, Carter T.; Hart, P. J.; LaPointe, Dennis

    2015-01-01

    Wildlife diseases can present significant threats to ecological systems and biological diversity, as well as domestic animal and human health. However, determining the dynamics of wildlife diseases and understanding the impact on host populations is a significant challenge. In Hawai‘i, there is ample circumstantial evidence that introduced avian malaria (Plasmodium relictum) has played an important role in the decline and extinction of many native forest birds. However, few studies have attempted to estimate disease transmission and mortality, survival, and individual species impacts in this distinctive ecosystem. We combined multi-state capture-recapture (longitudinal) models with cumulative age-prevalence (cross-sectional) models to evaluate these patterns in Apapane, Hawai‘i Amakihi, and Iiwi in low-, mid-, and high-elevation forests on the island of Hawai‘i based on four longitudinal studies of 3–7 years in length. We found species-specific patterns of malaria prevalence, transmission, and mortality rates that varied among elevations, likely in response to ecological factors that drive mosquito abundance. Malaria infection was highest at low elevations, moderate at mid elevations, and limited in high-elevation forests. Infection rates were highest for Iiwi and Apapane, likely contributing to the absence of these species in low-elevation forests. Adult malaria fatality rates were highest for Iiwi, intermediate for Amakihi at mid and high elevations, and lower for Apapane; low-elevation Amakihi had the lowest malaria fatality, providing strong evidence of malaria tolerance in this low-elevation population. Our study indicates that hatch-year birds may have greater malaria infection and/or fatality rates than adults. Our study also found that mosquitoes prefer feeding on Amakihi rather than Apapane, but Apapane are likely a more important reservoir for malaria transmission to mosquitoes. Our approach, based on host abundance and infection rates, may be an

  6. Reduction of a single granule drying model: An essential step in preparation of a population balance model with a continuous growth term

    DEFF Research Database (Denmark)

    Mortier, Séverine Thérèse F.C.; Daele, Timothy, Van; Gernaey, Krist V.

    2013-01-01

    in the reduced model. Simulations of the complex drying model were, in a next phase, used to develop the reduced model, which describes the decrease of the moisture content in function of the gas temperature. The developed reduced model was then included in a Population Balance Equation (PBE) to describe......The development of a Population Balance Model (PBM) for a pharmaceutical granule drying process requires a continuous growth term; the latter actually represents the drying process as the moisture content is the internal coordinate of the PBM. To establish such a PBM, a complex drying model...

  7. Species distribution modelling for conservation of an endangered endemic orchid.

    Science.gov (United States)

    Wang, Hsiao-Hsuan; Wonkka, Carissa L; Treglia, Michael L; Grant, William E; Smeins, Fred E; Rogers, William E

    2015-04-21

    Concerns regarding the long-term viability of threatened and endangered plant species are increasingly warranted given the potential impacts of climate change and habitat fragmentation on unstable and isolated populations. Orchidaceae is the largest and most diverse family of flowering plants, but it is currently facing unprecedented risks of extinction. Despite substantial conservation emphasis on rare orchids, populations continue to decline. Spiranthes parksii (Navasota ladies' tresses) is a federally and state-listed endangered terrestrial orchid endemic to central Texas. Hence, we aimed to identify potential factors influencing the distribution of the species, quantify the relative importance of each factor and determine suitable habitat for future surveys and targeted conservation efforts. We analysed several geo-referenced variables describing climatic conditions and landscape features to identify potential factors influencing the likelihood of occurrence of S. parksii using boosted regression trees. Our model classified 97 % of the cells correctly with regard to species presence and absence, and indicated that probability of existence was correlated with climatic conditions and landscape features. The most influential variables were mean annual precipitation, mean elevation, mean annual minimum temperature and mean annual maximum temperature. The most likely suitable range for S. parksii was the eastern portions of Leon and Madison Counties, the southern portion of Brazos County, a portion of northern Grimes County and along the borders between Burleson and Washington Counties. Our model can assist in the development of an integrated conservation strategy through: (i) focussing future survey and research efforts on areas with a high likelihood of occurrence, (ii) aiding in selection of areas for conservation and restoration and (iii) framing future research questions including those necessary for predicting responses to climate change. Our model could also

  8. Things fall apart: biological species form unconnected parsimony networks.

    Science.gov (United States)

    Hart, Michael W; Sunday, Jennifer

    2007-10-22

    The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.

  9. Considering transient population dynamics in the conservation of slow life-history species: An application to the sandhill crane

    Science.gov (United States)

    Gerber, Brian D.; Kendall, William L.

    2016-01-01

    The importance of transient dynamics of structured populations is increasingly recognized in ecology, yet these implications are not largely considered in conservation practices. We investigate transient and long-term population dynamics to demonstrate the process and utility of incorporating transient dynamics into conservation research and to better understand the population management of slow life-history species; these species can be theoretically highly sensitive to short- and long-term transient effects. We are specifically interested in the effects of anthropogenic removal of individuals from populations, such as caused by harvest, poaching, translocation, or incidental take. We use the sandhill crane (Grus canadensis) as an exemplar species; it is long-lived, has low reproduction, late maturity, and multiple populations are subject to sport harvest. We found sandhill cranes to have extremely high potential, but low likelihood for transient dynamics, even when the population is being harvested. The typically low population growth rate of slow life-history species appears to buffer against many perturbations causing large transient effects. Transient dynamics will dominate population trajectories of these species when stage structures are highly biased towards the younger and non-reproducing individuals, a situation that may be rare in established populations of long-lived animals. However, short-term transient population growth can be highly sensitive to vital rates that are relatively insensitive under equilibrium, suggesting that stage structure should be known if perturbation analysis is used to identify effective conservation strategies. For populations of slow life-history species that are not prone to large perturbations to their most productive individuals, population growth may be approximated by equilibrium dynamics.

  10. Border Collision Bifurcations in a Generalized Model of Population Dynamics

    Directory of Open Access Journals (Sweden)

    Lilia M. Ladino

    2016-01-01

    Full Text Available We analyze the dynamics of a generalized discrete time population model of a two-stage species with recruitment and capture. This generalization, which is inspired by other approaches and real data that one can find in literature, consists in considering no restriction for the value of the two key parameters appearing in the model, that is, the natural death rate and the mortality rate due to fishing activity. In the more general case the feasibility of the system has been preserved by posing opportune formulas for the piecewise map defining the model. The resulting two-dimensional nonlinear map is not smooth, though continuous, as its definition changes as any border is crossed in the phase plane. Hence, techniques from the mathematical theory of piecewise smooth dynamical systems must be applied to show that, due to the existence of borders, abrupt changes in the dynamic behavior of population sizes and multistability emerge. The main novelty of the present contribution with respect to the previous ones is that, while using real data, richer dynamics are produced, such as fluctuations and multistability. Such new evidences are of great interest in biology since new strategies to preserve the survival of the species can be suggested.

  11. Genetical structure of populations of modelling species of terrestrial mollusks in conditions of the urbanized landscape on example Сhondrula tridens Müll (Gastropoda, Pulmonata

    Directory of Open Access Journals (Sweden)

    Eduard A Snegin

    2011-06-01

    Full Text Available On the basis of the analysis of the morphological and genetical variability revealed by a method of gel-electrophoresis of proteins in PAAG, the state of gene pools of populations of modeling species Сhondrula tridens Müll (threedens snail in conditions of the urbanized forest-steppe landscape of the south of Mid-Russia Upland is investigated. In the majority of the investigated bunches authentic decrease of a level of heterozygosity and the decrease of an allelic diversification caused, both is fixed by natural historical factors, and factors of an anthropogenic parentage. The genetic-automatic processes in populations are considered and vectors of natural selection are defined. Calculation of effective number of researched bunches is spent.

  12. Non-Tuberculous Mycobacteria multispecies biofilms in cystic fibrosis: development of an in vitro Mycobacterium abscessus and Pseudomonas aeruginosa dual species biofilm model.

    Science.gov (United States)

    Rodríguez-Sevilla, Graciela; García-Coca, Marta; Romera-García, David; Aguilera-Correa, John Jairo; Mahíllo-Fernández, Ignacio; Esteban, Jaime; Pérez-Jorge, Concepción

    2018-04-01

    Lung disease in cystic fibrosis (CF) is characterized by the progressive colonization of the respiratory tract by different bacteria, which develop polymicrobial biofilms. In the past decades, there has been an increase in the number of CF patients infected with Non-Tuberculous Mycobacteria (NTM). Although Mycobacterium abscessus is the main NTM isolated globally, little is known about M. abscessus multispecies biofilm formation. In the present study we developed an in vitro model to study the phenotypic characteristics of biofilms formed by M. abscessus and Pseudomonas aeruginosa, a major pathogen in CF. For that purpose, dual species biofilms were grown on polycarbonate membranes with a fixed concentration of P. aeruginosa and different inoculums of M. abscessus. The biofilms were sampled at 24, 48, and 72 h and bacteria were quantified in specific media. The results revealed that the increasing initial concentration of M. abscessus in dual species biofilms had an effect on its population only at 24 and 48 h, whereas P. aeruginosa was not affected by the different concentrations used of M. abscessus. Time elapsed increased biofilm formation of both species, specially between 24 and 48 h. According to the results, the conditions to produce a mature dual species biofilm in which the relative species distribution remained stable were 72 h growth of the mixed microbial culture at a 1:1 ratio. A significant decrease in mycobacterial population in dual compared to single species biofilms was found, suggesting that P. aeruginosa has a negative influence on M. abscessus. Finally, in a proof of concept experiment, young and mature dual species biofilms were exposed to clarithromycin. Copyright © 2018 Elsevier GmbH. All rights reserved.

  13. Critical Domain Problem for the Reaction–Telegraph Equation Model of Population Dynamics

    Directory of Open Access Journals (Sweden)

    Weam Alharbi

    2018-04-01

    Full Text Available A telegraph equation is believed to be an appropriate model of population dynamics as it accounts for the directional persistence of individual animal movement. Being motivated by the problem of habitat fragmentation, which is known to be a major threat to biodiversity that causes species extinction worldwide, we consider the reaction–telegraph equation (i.e., telegraph equation combined with the population growth on a bounded domain with the goal to establish the conditions of species survival. We first show analytically that, in the case of linear growth, the expression for the domain’s critical size coincides with the critical size of the corresponding reaction–diffusion model. We then consider two biologically relevant cases of nonlinear growth, i.e., the logistic growth and the growth with a strong Allee effect. Using extensive numerical simulations, we show that in both cases the critical domain size of the reaction–telegraph equation is larger than the critical domain size of the reaction–diffusion equation. Finally, we discuss possible modifications of the model in order to enhance the positivity of its solutions.

  14. Differences in a ribosomal DNA sequence of Strongylus species allows identification of single eggs.

    Science.gov (United States)

    Campbell, A J; Gasser, R B; Chilton, N B

    1995-03-01

    In the current study, molecular techniques were evaluated for the species identification of individual strongyle eggs. Adult worms of Strongylus edentatus, S. equinus and S. vulgaris were collected at necropsy from horses from Australia and the U.S.A. Genomic DNA was isolated and a ribosomal transcribed spacer (ITS-2) amplified and sequenced using polymerase chain reaction (PCR) techniques. The length of the ITS-2 sequence of S. edentatus, S. equinus and S. vulgaris ranged between 217 and 235 nucleotides. Extensive sequence analysis demonstrated a low degree (0-0.9%) of intraspecific variation in the ITS-2 for the Strongylus species examined, whereas the levels of interspecific differences (13-29%) were significantly greater. Interspecific differences in the ITS-2 sequences allowed unequivocal species identification of single worms and eggs using PCR-linked restriction fragment length polymorphism. These results demonstrate the potential of the ribosomal spacers as genetic markers for species identification of single strongyle eggs from horse faeces.

  15. Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

    Directory of Open Access Journals (Sweden)

    Yu-Bin Yan

    2016-09-01

    Full Text Available Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, R. mucronata, and R. stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

  16. Potential DNA barcodes for Melilotus species based on five single loci and their combinations.

    Directory of Open Access Journals (Sweden)

    Fan Wu

    Full Text Available Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production.

  17. Study of GABAergic extra-synaptic tonic inhibition in single neurons and neural populations by traversing neural scales: application to propofol-induced anaesthesia.

    Science.gov (United States)

    Hutt, Axel; Buhry, Laure

    2014-12-01

    Anaesthetic agents are known to affect extra-synaptic GABAergic receptors, which induce tonic inhibitory currents. Since these receptors are very sensitive to small concentrations of agents, they are supposed to play an important role in the underlying neural mechanism of general anaesthesia. Moreover anaesthetic agents modulate the encephalographic activity (EEG) of subjects and hence show an effect on neural populations. To understand better the tonic inhibition effect in single neurons on neural populations and hence how it affects the EEG, the work considers single neurons and neural populations in a steady-state and studies numerically and analytically the modulation of their firing rate and nonlinear gain with respect to different levels of tonic inhibition. We consider populations of both type-I (Leaky Integrate-and-Fire model) and type-II (Morris-Lecar model) neurons. To bridge the single neuron description to the population description analytically, a recently proposed statistical approach is employed which allows to derive new analytical expressions for the population firing rate for type-I neurons. In addition, the work shows the derivation of a novel transfer function for type-I neurons as considered in neural mass models and studies briefly the interaction of synaptic and extra-synaptic inhibition. We reveal a strong subtractive and divisive effect of tonic inhibition in type-I neurons, i.e. a shift of the firing rate to higher excitation levels accompanied by a change of the nonlinear gain. Tonic inhibition shortens the excitation window of type-II neurons and their populations while maintaining the nonlinear gain. The gained results are interpreted in the context of recent experimental findings under propofol-induced anaesthesia.

  18. Plant Mating Systems Often Vary Widely Among Populations

    Directory of Open Access Journals (Sweden)

    Michael R. Whitehead

    2018-04-01

    Full Text Available Most flowering plants are hermaphroditic, yet the proportion of seeds fertilized by self and outcross pollen varies widely among species, ranging from predominant self-fertilization to exclusive outcrossing. A population's rate of outcrossing has important evolutionary outcomes as it influences genetic structure, effective population size, and offspring fitness. Because most mating system studies have quantified outcrossing rates for just one or two populations, past reviews of mating system diversity have not been able to characterize the extent of variation among populations. Here we present a new database of more than 30 years of mating system studies that report outcrossing rates for three or more populations per species. This survey, which includes 741 populations from 105 species, illustrates substantial and prevalent among-population variation in the mating system. Intermediate outcrossing rates (mixed mating are common; 63% of species had at least one mixed mating population. The variance among populations and within species was not significantly correlated with pollination mode or phylogeny. Our review underscores the need for studies exploring variation in the relative influence of ecological and genetic factors on the mating system, and how this varies among populations. We conclude that estimates of outcrossing rates from single populations are often highly unreliable indicators of the mating system of an entire species.

  19. Reactive oxygen species formation during tetanic contractions in single isolated Xenopus myofibers

    OpenAIRE

    Zuo, Li; Nogueira, Leonardo; Hogan, Michael C.

    2011-01-01

    Contracting skeletal muscle produces reactive oxygen species (ROS) that have been shown to affect muscle function and adaptation. However, real-time measurement of ROS in contracting myofibers has proven to be difficult. We used amphibian (Xenopus laevis) muscle to test the hypothesis that ROS are formed during contractile activity in isolated single skeletal muscle fibers and that this contraction-induced ROS formation affects fatigue development. Single myofibers were loaded with 5 μM dihyd...

  20. Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide.

    Science.gov (United States)

    Baeza, J Antonio; Behringer, Donald C

    2017-01-01

    The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi , an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni . Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across  550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.

  1. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    Directory of Open Access Journals (Sweden)

    Zak Frentz

    2015-10-01

    Full Text Available Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

  2. Interspecific introgression and changes in population structure in a flatfish species complex after the Prestige accident

    International Nuclear Information System (INIS)

    Crego-Prieto, V.; Danancher, D.; Campo, D.; Perez, J.; Garcia-Vazquez, E.; Roca, A.

    2013-01-01

    Highlights: • Impact of Prestige oil spill was studied on two sympatric megrim fish populations. • Samples before and nine years after the accident were genetically analyzed. • A large proportion of post-F1 interspecific hybrids was found in the polluted area. • Both species’ population structure was altered by introgression of foreign alleles. • The spillage likely promoted a hybrid zone for Lepidorhombus in the areas affected. -- Abstract: Oil spills cause aggressive impacts on marine ecosystems affecting immense areas and the species inhabiting them. If wastes are not cleaned up properly, the remnants may affect local populations for a long time. This work focuses on the long-term impacts of the Prestige spillage that occurred off Galician coast (Spain) in November 2002. Model species were two sympatric flatfish, the megrims Lepidorhombus whiffiagonis and Lepidorhombus boscii. Samples obtained before and nine years after the Prestige accident from affected and unaffected areas were genotyped for six hypervariable nuclear markers and for the mitochondrial D-loop sequence. The results revealed a high proportion of post-F1 interspecific hybrids in the area affected, and also increased intraspecific population differentiation likely due to such localized introgression of foreign genes. These changes suggest the appearance of a hybrid zone following the accident and emphasize the need of paying special attention to potential evolutionary impacts of oil spills

  3. In vitro evaluation of single- and multi-strain probiotics: Inter-species inhibition between probiotic strains, and inhibition of pathogens.

    Science.gov (United States)

    Chapman, C M C; Gibson, G R; Rowland, I

    2012-08-01

    Many studies comparing the effects of single- and multi-strain probiotics on pathogen inhibition compare treatments with different concentrations. They also do not examine the possibility of inhibition between probiotic strains with a mixture. We tested the ability of 14 single-species probiotics to inhibit each other using a cross-streak assay, and agar spot test. We then tested the ability of 15 single-species probiotics and 5 probiotic mixtures to inhibit Clostridium difficile, Escherichia coli and S. typhimurium, using the agar spot test. Testing was done with mixtures created in two ways: one group contained component species incubated together, the other group of mixtures was made using component species which had been incubated separately, equalised to equal optical density, and then mixed in equal volumes. Inhibition was observed for all combinations of probiotics, suggesting that when used as such there may be inhibition between probiotics, potentially reducing efficacy of the mixture. Significant inter-species variation was seen against each pathogen. When single species were tested against mixtures, the multi-species preparations displayed significantly (p probiotic species will inhibit each other when incubated together in vitro, in many cases a probiotic mixture was more effective at inhibiting pathogens than its component species when tested at approximately equal concentrations of biomass. This suggests that using a probiotic mixture might be more effective at reducing gastrointestinal infections, and that creating a mixture using species with different effects against different pathogens may have a broader spectrum of action that a single provided by a single strain. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Extinction risk assessment for the species survival plan (SSP) population of the Bali mynah (Leucopsar rothschildi).

    Science.gov (United States)

    Earnhardt, Joanne M; Thompson, Steven D; Faust, Lisa J

    2009-05-01

    The Bali mynah Species Survival Plan (SSP), an Association of Zoos and Aquariums program, strives to maintain the genetic and demographic health of its population, avoid unplanned changes in size, and minimize the risk of population extinction. The SSP population meets current demographic and genetic objectives with a population size of 209 birds at 61 institutions and 96% genetic diversity (GD) retained from the source population. However, participating institutions have expressed concerns regarding space allocation, target population size (TPS), breeding restrictions, inbreeding depression, and harvest in relation to future population availability and viability. Based on these factors, we assess five questions with a quantitative risk assessment, specifically a population viability analysis (PVA) using ZooRisk software. Using an individual-based stochastic model, we project potential population changes under different conditions (e.g. changes in TPS and genetic management) to identify the most effective management actions. Our projections indicate that under current management conditions, population decline and extinction are unlikely and that although GD will decline over 100 years the projected loss does not exceed levels acceptable to population managers (less than 90% GD retained). Model simulations indicate that the combination of two genetic management strategies (i.e. priority breeding based on mean kinship and inbreeding avoidance) benefits the retention of GD and reduces the accumulation of inbreeding. The current TPS (250) is greater than necessary to minimize the risk of extinction for the SSP population but any reduction in TPS must be accompanied by continued application of genetic management. If carefully planned, birds can be harvested for transfer to Bali for a reintroduction program without jeopardizing the SSP population.

  5. First record of Wolbachia in South American terrestrial isopods: prevalence and diversity in two species of Balloniscus (Crustacea, Oniscidea

    Directory of Open Access Journals (Sweden)

    Mauricio Pereira Almerão

    2012-01-01

    Full Text Available Wolbachia are endosymbiotic bacteria that commonly infect arthropods, inducing certain phenotypes in their hosts. So far, no endemic South American species of terrestrial isopods have been investigated for Wolbachia infection. In this work, populations from two species of Balloniscus (B. sellowii and B. glaber were studied through a diagnostic PCR assay. Fifteen new Wolbachia 16S rDNA sequences were detected. Wolbachia found in both species were generally specific to one population, and five populations hosted two different Wolbachia 16S rDNA sequences. Prevalence was higher in B. glaber than in B. sellowii, but uninfected populations could be found in both species. Wolbachia strains from B. sellowii had a higher genetic variation than those isolated from B. glaber. AMOVA analyses showed that most of the genetic variance was distributed among populations of each species rather than between species, and the phylogenetic analysis suggested that Wolbachia strains from Balloniscus cluster within Supergroup B, but do not form a single monophyletic clade, suggesting multiple infections for this group. Our results highlight the importance of studying Wolbachia prevalence and genetic diversity in Neotropical species and suggest that South American arthropods may harbor a great number of diverse strains, providing an interesting model to investigate the evolution of Wolbachia and its hosts.

  6. Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae, Rhodophyta) from New Zealand.

    Science.gov (United States)

    Muangmai, Narongrit; Fraser, Ceridwen I; Zuccarello, Giuseppe C

    2015-06-01

    Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct "cryptic" species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa. © 2015 Phycological Society of America.

  7. Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.

    Science.gov (United States)

    Schmidt-Lebuhn, Alexander N; Aitken, Nicola C; Chuah, Aaron

    2017-11-01

    Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele

  8. New trends in species distribution modelling

    Science.gov (United States)

    Zimmermann, Niklaus E.; Edwards, Thomas C.; Graham, Catherine H.; Pearman, Peter B.; Svenning, Jens-Christian

    2010-01-01

    Species distribution modelling has its origin in the late 1970s when computing capacity was limited. Early work in the field concentrated mostly on the development of methods to model effectively the shape of a species' response to environmental gradients (Austin 1987, Austin et al. 1990). The methodology and its framework were summarized in reviews 10–15 yr ago (Franklin 1995, Guisan and Zimmermann 2000), and these syntheses are still widely used as reference landmarks in the current distribution modelling literature. However, enormous advancements have occurred over the last decade, with hundreds – if not thousands – of publications on species distribution model (SDM) methodologies and their application to a broad set of conservation, ecological and evolutionary questions. With this special issue, originating from the third of a set of specialized SDM workshops (2008 Riederalp) entitled 'The Utility of Species Distribution Models as Tools for Conservation Ecology', we reflect on current trends and the progress achieved over the last decade.

  9. A multistage decision support framework to guide tree species management under climate change via habitat suitability and colonization models, and a knowledge-based scoring system

    Science.gov (United States)

    Anantha M. Prasad; Louis R. Iverson; Stephen N. Matthews; Matthew P. Peters

    2016-01-01

    Context. No single model can capture the complex species range dynamics under changing climates--hence the need for a combination approach that addresses management concerns. Objective. A multistage approach is illustrated to manage forested landscapes under climate change. We combine a tree species habitat model--DISTRIB II, a species colonization model--SHIFT, and...

  10. Using mitochondrial and nuclear sequence data for disentangling population structure in complex pest species: a case study with Dermanyssus gallinae.

    Directory of Open Access Journals (Sweden)

    Lise Roy

    Full Text Available Among global changes induced by human activities, association of breakdown of geographical barriers and impoverishered biodiversity of agroecosystems may have a strong evolutionary impact on pest species. As a consequence of trade networks' expansion, secondary contacts between incipient species, if hybrid incompatibility is not yet reached, may result in hybrid swarms, even more when empty niches are available as usual in crop fields and farms. By providing important sources of genetic novelty for organisms to adapt in changing environments, hybridization may be strongly involved in the emergence of invasive populations. Because national and international trade networks offered multiple hybridization opportunities during the previous and current centuries, population structure of many pest species is expected to be the most intricate and its inference often blurred when using fast-evolving markers. Here we show that mito-nuclear sequence datasets may be the most helpful in disentangling successive layers of admixture in the composition of pest populations. As a model we used D. gallinae s. l., a mesostigmatid mite complex of two species primarily parasitizing birds, namely D. gallinae L1 and D. gallinae s. str. The latter is a pest species, considered invading layer farms in Brazil. The structure of the pest as represented by isolates from both wild and domestic birds, from European (with a focus on France, Australian and Brazilian farms, revealed past hybridization events and very recent contact between deeply divergent lineages. The role of wild birds in the dissemination of mites appears to be null in European and Australian farms, but not in Brazilian ones. In French farms, some recent secondary contact is obviously consecutive to trade flows. Scenarios of populations' history were established, showing five different combinations of more or less dramatic bottlenecks and founder events, nearly interspecific hybridizations and recent

  11. Defining population structure and genetic signatures of decline in the giant garter snake (Thamnophis gigas): implications for conserving threatened species within highly altered landscapes

    Science.gov (United States)

    Wood, Dustin A.; Halstead, Brian J.; Casazza, Michael L.; Hansen, Eric C.; Wylie, Glenn D.; Vandergast, Amy

    2015-01-01

    Anthropogenic habitat fragmentation can disrupt the ability of species to disperse across landscapes, which can alter the levels and distribution of genetic diversity within populations and negatively impact long-term viability. The giant gartersnake (Thamnophis gigas) is a state and federally threatened species that historically occurred in the wetland habitats of California’s Great Central Valley. Despite the loss of 93 % of historic wetlands throughout the Central Valley, giant gartersnakes continue to persist in relatively small, isolated patches of highly modified agricultural wetlands. Gathering information regarding genetic diversity and effective population size represents an essential component for conservation management programs aimed at this species. Previous mitochondrial sequence studies have revealed historical patterns of differentiation, yet little is known about contemporary population structure and diversity. On the basis of 15 microsatellite loci, we estimate population structure and compare indices of genetic diversity among populations spanning seven drainage basins within the Central Valley. We sought to understand how habitat loss may have affected genetic differentiation, genetic diversity and effective population size, and what these patterns suggest in terms of management and restoration actions. We recovered five genetic clusters that were consistent with regional drainage basins, although three northern basins within the Sacramento Valley formed a single genetic cluster. Our results show that northern drainage basin populations have higher connectivity than among central and southern basins populations, and that greater differentiation exists among the more geographically isolated populations in the central and southern portion of the species’ range. Genetic diversity measures among basins were significantly different, and were generally lower in southern basin populations. Levels of inbreeding and evidence of population

  12. Allocating conservation resources between areas where persistence of a species is uncertain.

    Science.gov (United States)

    McDonald-Madden, Eve; Chadès, Iadine; McCarthy, Michael A; Linkie, Matthew; Possingham, Hugh P

    2011-04-01

    Research on the allocation of resources to manage threatened species typically assumes that the state of the system is completely observable; for example whether a species is present or not. The majority of this research has converged on modeling problems as Markov decision processes (MDP), which give an optimal strategy driven by the current state of the system being managed. However, the presence of threatened species in an area can be uncertain. Typically, resource allocation among multiple conservation areas has been based on the biggest expected benefit (return on investment) but fails to incorporate the risk of imperfect detection. We provide the first decision-making framework for confronting the trade-off between information and return on investment, and we illustrate the approach for populations of the Sumatran tiger (Panthera tigris sumatrae) in Kerinci Seblat National Park. The problem is posed as a partially observable Markov decision process (POMDP), which extends MDP to incorporate incomplete detection and allows decisions based on our confidence in particular states. POMDP has previously been used for making optimal management decisions for a single population of a threatened species. We extend this work by investigating two populations, enabling us to explore the importance of variation in expected return on investment between populations on how we should act. We compare the performance of optimal strategies derived assuming complete (MDP) and incomplete (POMDP) observability. We find that uncertainty about the presence of a species affects how we should act. Further, we show that assuming full knowledge of a species presence will deliver poorer strategic outcomes than if uncertainty about a species status is explicitly considered. MDP solutions perform up to 90% worse than the POMDP for highly cryptic species, and they only converge in performance when we are certain of observing the species during management: an unlikely scenario for many

  13. Mortality in single fathers compared with single mothers and partnered parents: a population-based cohort study.

    Science.gov (United States)

    Chiu, Maria; Rahman, Farah; Vigod, Simone; Lau, Cindy; Cairney, John; Kurdyak, Paul

    2018-03-01

    Single parent families, including families headed by single fathers, are becoming increasingly common around the world. Previous evidence suggests that single parenthood is associated with adverse health outcomes and increased mortality; however, most studies have focused on single mothers, with little known about the health of single fathers. This study aimed to examine mortality in a large population-based sample of Canadian single fathers compared with single mothers and partnered fathers and mothers. We used a representative sample of 871 single fathers, 4590 single mothers, 16 341 partnered fathers, and 18 688 partnered mothers from the Canadian Community Health Survey (cycles 2001-12; earliest survey date: Sept 5, 2000; latest survey date: Dec 24, 2012). We anonymously linked survey participants to health administrative database records to ascertain health status at baseline and mortality from survey date up to Oct 28, 2016. We included individuals who were aged 15 years or older, living in a household with one or more biological or adopted child younger than 25 years, and living in Ontario, and we excluded those who left Ontario during the study period or had data discrepancies. Single parents were defined as those who were divorced, separated, widowed, or single, never-married, and non-cohabitating, and partnered parents were defined as those who were married or common-law partners. We investigated differences in mortality using Cox proportional hazards models with adjustment for sociodemographic, lifestyle, and clinical factors. Median follow-up was 11·10 years (IQR 7·36-13·54). Mortality in single fathers (5·8 per 1000 person-years) was three-times higher than rates in single mothers (1·74 per 1000 person-years) and partnered fathers (1·94 per 1000 person-years). Single fathers had a significantly higher adjusted risk of dying than both single mothers (hazard ratio [HR] 2·49, 95% CI 1·20-5·15; p=0·01) and partnered fathers (2·06, 1·11-3

  14. Global sensitivity analysis applied to drying models for one or a population of granules

    DEFF Research Database (Denmark)

    Mortier, Severine Therese F. C.; Gernaey, Krist; Thomas, De Beer

    2014-01-01

    The development of mechanistic models for pharmaceutical processes is of increasing importance due to a noticeable shift toward continuous production in the industry. Sensitivity analysis is a powerful tool during the model building process. A global sensitivity analysis (GSA), exploring sensitiv......The development of mechanistic models for pharmaceutical processes is of increasing importance due to a noticeable shift toward continuous production in the industry. Sensitivity analysis is a powerful tool during the model building process. A global sensitivity analysis (GSA), exploring...... sensitivity in a broad parameter space, is performed to detect the most sensitive factors in two models, that is, one for drying of a single granule and one for the drying of a population of granules [using population balance model (PBM)], which was extended by including the gas velocity as extra input...... compared to our earlier work. beta(2) was found to be the most important factor for the single particle model which is useful information when performing model calibration. For the PBM-model, the granule radius and gas temperature were found to be most sensitive. The former indicates that granulator...

  15. Incorporating spatial autocorrelation into species distribution models alters forecasts of climate-mediated range shifts.

    Science.gov (United States)

    Crase, Beth; Liedloff, Adam; Vesk, Peter A; Fukuda, Yusuke; Wintle, Brendan A

    2014-08-01

    Species distribution models (SDMs) are widely used to forecast changes in the spatial distributions of species and communities in response to climate change. However, spatial autocorrelation (SA) is rarely accounted for in these models, despite its ubiquity in broad-scale ecological data. While spatial autocorrelation in model residuals is known to result in biased parameter estimates and the inflation of type I errors, the influence of unmodeled SA on species' range forecasts is poorly understood. Here we quantify how accounting for SA in SDMs influences the magnitude of range shift forecasts produced by SDMs for multiple climate change scenarios. SDMs were fitted to simulated data with a known autocorrelation structure, and to field observations of three mangrove communities from northern Australia displaying strong spatial autocorrelation. Three modeling approaches were implemented: environment-only models (most frequently applied in species' range forecasts), and two approaches that incorporate SA; autologistic models and residuals autocovariate (RAC) models. Differences in forecasts among modeling approaches and climate scenarios were quantified. While all model predictions at the current time closely matched that of the actual current distribution of the mangrove communities, under the climate change scenarios environment-only models forecast substantially greater range shifts than models incorporating SA. Furthermore, the magnitude of these differences intensified with increasing increments of climate change across the scenarios. When models do not account for SA, forecasts of species' range shifts indicate more extreme impacts of climate change, compared to models that explicitly account for SA. Therefore, where biological or population processes induce substantial autocorrelation in the distribution of organisms, and this is not modeled, model predictions will be inaccurate. These results have global importance for conservation efforts as inaccurate

  16. Modelling population-level consequences of chronic external gamma irradiation in aquatic invertebrates under laboratory conditions

    Energy Technology Data Exchange (ETDEWEB)

    Lance, Emilie [Laboratoire de modelisation pour l' expertise environnementale (LM2E) Institut de Radioprotection et de Surete Nucleaire (IRSN), PRP-ENV, SERIS, Cadarache (France); Alonzo, Frederic, E-mail: frederic.alonzo@irsn.fr [Laboratoire d' ecotoxicologie des radionucleides (LECO) Institut de Radioprotection et de Surete Nucleaire (IRSN), PRP-ENV, SERIS, Cadarache (France); Garcia-Sanchez, Laurent [Laboratoire de biogeochimie, biodisponibilite et transferts des radionucleides (L2BT) Institut de Radioprotection et de Surete Nucleaire (IRSN), PRP-ENV, SERIS, Cadarache (France); Beaugelin-Seiller, Karine; Garnier-Laplace, Jacqueline [Laboratoire de modelisation pour l' expertise environnementale (LM2E) Institut de Radioprotection et de Surete Nucleaire (IRSN), PRP-ENV, SERIS, Cadarache (France)

    2012-07-01

    We modelled population-level consequences of chronic external gamma irradiation in aquatic invertebrates under laboratory conditions. We used Leslie matrices to combine life-history characteristics (duration of life stages, survival and fecundity rates) and dose rate-response curves for hatching, survival and reproduction fitted on effect data from the FREDERICA database. Changes in net reproductive rate R{sub 0} (offspring per individual) and asymptotic population growth rate {lambda} (dimensionless) were calculated over a range of dose rates in two marine polychaetes (Neanthes arenaceodentata and Ophryotrocha diadema) and a freshwater gastropod (Physa heterostropha). Sensitivities in R{sub 0} and {lambda} to changes in life-history traits were analysed in each species. Results showed that fecundity has the strongest influence on R{sub 0}. A delay in age at first reproduction is most critical for {lambda} independent of the species. Fast growing species were proportionally more sensitive to changes in individual endpoints than slow growing species. Reduction of 10% in population {lambda} were predicted at dose rates of 6918, 5012 and 74,131 {mu}Gy{center_dot}h{sup -1} in N. arenaceodentata, O. diadema and P. heterostropha respectively, resulting from a combination of strong effects on several individual endpoints in each species. These observations made 10%-reduction in {lambda} a poor criterion for population protection. The lowest significant changes in R{sub 0} and {lambda} were respectively predicted at a same dose rate of 1412 {mu}Gy h{sup -1} in N. arenaceodentata, at 760 and 716 {mu}Gy h{sup -1} in O. diadema and at 12,767 and 13,759 {mu}Gy h{sup -1} in P. heterostropha. These values resulted from a combination of slight but significant changes in several measured endpoints and were lower than effective dose rates calculated for the individual level in O. diadema and P. heterostropha. The relevance of the experimental dataset (external irradiation rather

  17. Assessing the status and trend of bat populations across broad geographic regions with dynamic distribution models

    Science.gov (United States)

    Rodhouse, Thomas J.; Ormsbee, Patricia C.; Irvine, Kathryn M.; Vierling, Lee A.; Szewczak, Joseph M.; Vierling, Kerri T.

    2012-01-01

    Bats face unprecedented threats from habitat loss, climate change, disease, and wind power development, and populations of many species are in decline. A better ability to quantify bat population status and trend is urgently needed in order to develop effective conservation strategies. We used a Bayesian autoregressive approach to develop dynamic distribution models for Myotis lucifugus, the little brown bat, across a large portion of northwestern USA, using a four-year detection history matrix obtained from a regional monitoring program. This widespread and abundant species has experienced precipitous local population declines in northeastern USA resulting from the novel disease white-nose syndrome, and is facing likely range-wide declines. Our models were temporally dynamic and accounted for imperfect detection. Drawing on species–energy theory, we included measures of net primary productivity (NPP) and forest cover in models, predicting that M. lucifugus occurrence probabilities would covary positively along those gradients.

  18. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

    Science.gov (United States)

    Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

    2015-09-15

    There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

  19. Population genetics of four heavily exploited shark species around the Arabian Peninsula

    KAUST Repository

    Spaet, Julia L.Y.

    2015-05-01

    The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.

  20. Molecular identification of broomrape species from a single seed by High Resolution Melting analysis

    Directory of Open Access Journals (Sweden)

    Mathieu Rolland

    2016-12-01

    Full Text Available Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (P. aegyptiaca, O. cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa from a single seed. Based on trnL and rbcL plastidial genes amplification, the designed assay successfully identifies O. cumana, O. cernua, O. crenata, O. minor, O. hederae, and O. foetida; P. ramosa and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90 %. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples. The described assay fulfils its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material.

  1. Conservation state of populations of rare plant species in highly transformed meadow steppes of Southern Opillya

    Directory of Open Access Journals (Sweden)

    I. I. Dmytrash-Vatseba

    2016-09-01

    Full Text Available Degradation of natural habitats causes rapid extinction of rare plant populations. The diversity of rare plant species in the meadow steppes of Southern Opillya (Western Ukraine depends strongly on patch area, pasture digression of vegetation and a variety of eco-coenotical conditions. The main threats for the rare components of the meadow steppe flora are reduction of habitat and overgrazing. Spatial connections between sites are unable to support a constant rare plant population. The analysis of the composition of rare plant meadow-steppe species indicated that habitats with similar rare species composition usually have similar parameters of area, stages of pasture digression and eco-coenotical conditions. Spatial connectivity of patches does not ensure species similarity of rare components of the flora. Rare plant species were grouped according to their preferences for habitat , area and condition. In small patches subject to any stage of pasture digression grow populations of Adonis vernalis L., Pulsatilla patens (L. Mill., P. grandis Wender., Stipa capillata L., S. рennata L., Chamaecytisus blockianus (Pawł. Klásková etc. On the contrary, populations of other species (Carlina onopordifolia Besser. ex Szafer., Kuecz. et Pawł., Adenophora liliifolia (L. Ledeb. ex A. DC., Crambe tataria Sebeók, Euphorbia volhynica Besser ex Racib., Stipa tirsa Stev. etc. prefer large habitats, not changed by pasture digression. Prevention of reduction of rare species diversity requires preservation (also extension of patch area and regulation of grazing intensity.

  2. Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

    DEFF Research Database (Denmark)

    Mailund, Thomas; Dutheil, Julien; Hobolth, Asger

    2011-01-01

    event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may......, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus......) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report...

  3. Lutzomyia longipalpis in Brazil: a complex or a single species? A mini-review

    Directory of Open Access Journals (Sweden)

    Luiz GSR Bauzer

    2007-02-01

    Full Text Available Lutzomyia longipalpis is the main vector of Leishmania infantum chagasi, the causative agent of American visceral leishmaniasis (AVL. Although there is strong evidence that Lu. longipalpis is a species complex, not all data concerning populations from Brazil support this hypothesis. The issue is still somewhat controversial for this large part of Lu. longipalpis distribution range even though that it is the Latin American region contributing to most of the cases of AVL. In this mini-review we consider in detail the current data for the Brazilian populations and conclude that Lu. longipalpis is a complex of incipient vector species with a complexity similar to Anopheles gambiae s.s. in Africa.

  4. Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species

    Directory of Open Access Journals (Sweden)

    Brewer Marin

    2010-09-01

    Full Text Available Abstract Background The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated. Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern

  5. Modelling planktic foraminifer growth and distribution using an ecophysiological multi-species approach

    Directory of Open Access Journals (Sweden)

    F. Lombard

    2011-04-01

    Full Text Available We present an eco-physiological model reproducing the growth of eight foraminifer species (Neogloboquadrina pachyderma, Neogloboquadrina incompta, Neogloboquadrina dutertrei, Globigerina bulloides, Globigerinoides ruber, Globigerinoides sacculifer, Globigerinella siphonifera and Orbulina universa. By using the main physiological rates of foraminifers (nutrition, respiration, symbiotic photosynthesis, this model estimates their growth as a function of temperature, light availability, and food concentration. Model parameters are directly derived or calibrated from experimental observations and only the influence of food concentration (estimated via Chlorophyll-a concentration was calibrated against field observations. Growth rates estimated from the model show positive correlation with observed abundance from plankton net data suggesting close coupling between individual growth and population abundance. This observation was used to directly estimate potential abundance from the model-derived growth. Using satellite data, the model simulate the dominant foraminifer species with a 70.5% efficiency when compared to a data set of 576 field observations worldwide. Using outputs of a biogeochemical model of the global ocean (PISCES instead of satellite images as forcing variables gives also good results, but with lower efficiency (58.9%. Compared to core tops observations, the model also correctly reproduces the relative worldwide abundance and the diversity of the eight species when using either satellite data either PISCES results. This model allows prediction of the season and water depth at which each species has its maximum abundance potential. This offers promising perspectives for both an improved quantification of paleoceanographic reconstructions and for a better understanding of the foraminiferal role in the marine carbon cycle.

  6. Scaling local species-habitat relations to the larger landscape with a hierarchical spatial count model

    Science.gov (United States)

    Thogmartin, W.E.; Knutson, M.G.

    2007-01-01

    Much of what is known about avian species-habitat relations has been derived from studies of birds at local scales. It is entirely unclear whether the relations observed at these scales translate to the larger landscape in a predictable linear fashion. We derived habitat models and mapped predicted abundances for three forest bird species of eastern North America using bird counts, environmental variables, and hierarchical models applied at three spatial scales. Our purpose was to understand habitat associations at multiple spatial scales and create predictive abundance maps for purposes of conservation planning at a landscape scale given the constraint that the variables used in this exercise were derived from local-level studies. Our models indicated a substantial influence of landscape context for all species, many of which were counter to reported associations at finer spatial extents. We found land cover composition provided the greatest contribution to the relative explained variance in counts for all three species; spatial structure was second in importance. No single spatial scale dominated any model, indicating that these species are responding to factors at multiple spatial scales. For purposes of conservation planning, areas of predicted high abundance should be investigated to evaluate the conservation potential of the landscape in their general vicinity. In addition, the models and spatial patterns of abundance among species suggest locations where conservation actions may benefit more than one species. ?? 2006 Springer Science+Business Media B.V.

  7. Climate, invasive species and land use drive population dynamics of a cold-water specialist

    Science.gov (United States)

    Kovach, Ryan P.; Al-Chokhachy, Robert K.; Whited, Diane C.; Schmetterling, David A.; Dux, Andrew M; Muhlfeld, Clint C.

    2017-01-01

    Climate change is an additional stressor in a complex suite of threats facing freshwater biodiversity, particularly for cold-water fishes. Research addressing the consequences of climate change on cold-water fish has generally focused on temperature limits defining spatial distributions, largely ignoring how climatic variation influences population dynamics in the context of other existing stressors.We used long-term data from 92 populations of bull trout Salvelinus confluentus – one of North America's most cold-adapted fishes – to quantify additive and interactive effects of climate, invasive species and land use on population dynamics (abundance, variability and growth rate).Populations were generally depressed, more variable and declining where spawning and rearing stream habitat was limited, invasive species and land use were prevalent and stream temperatures were highest. Increasing stream temperature acted additively and independently, whereas land use and invasive species had additive and interactive effects (i.e. the impact of one stressor depended on exposure to the other stressor).Most (58%–78%) of the explained variation in population dynamics was attributed to the presence of invasive species, differences in life history and management actions in foraging habitats in rivers, lakes and reservoirs. Although invasive fishes had strong negative effects on populations in foraging habitats, proactive control programmes appeared to effectively temper their negative impact.Synthesis and applications. Long-term demographic data emphasize that climate warming will exacerbate imperilment of cold-water specialists like bull trout, yet other stressors – especially invasive fishes – are immediate threats that can be addressed by proactive management actions. Therefore, climate-adaptation strategies for freshwater biodiversity should consider existing abiotic and biotic stressors, some of which provide potential and realized opportunity for conservation

  8. Species Distribution Modelling of Aedes aegypti in two dengue-endemic regions of Pakistan.

    Science.gov (United States)

    Fatima, Syeda Hira; Atif, Salman; Rasheed, Syed Basit; Zaidi, Farrah; Hussain, Ejaz

    2016-03-01

    Statistical tools are effectively used to determine the distribution of mosquitoes and to make ecological inferences about the vector-borne disease dynamics. In this study, we utilised species distribution models to understand spatial patterns of Aedes aegypti in two dengue-prevalent regions of Pakistan, Lahore and Swat. Species distribution models can potentially indicate the probability of suitability of Ae. aegypti once introduced to new regions like Swat, where invasion of this species is a recent phenomenon. The distribution of Ae. aegypti was determined by applying the MaxEnt algorithm on a set of potential environmental factors and species sample records. The ecological dependency of species on each environmental variable was analysed using response curves. We quantified the statistical performance of the models based on accuracy assessment and spatial predictions. Our results suggest that Ae. aegypti is widely distributed in Lahore. Human population density and urban infrastructure are primarily responsible for greater probability of mosquito occurrence in this region. In Swat, Ae. aegypti has clumped distribution, where urban patches provide refuge to the species in an otherwise hostile heterogeneous environment and road networks are assumed to have facilitated in passive-mediated dispersal of species. In Pakistan, Ae. aegypti is expanding its range northwards; this could be associated with rapid urbanisation, trade and travel. The main implication of this expansion is that more people are at risk of dengue fever in the northern highlands of Pakistan. © 2016 John Wiley & Sons Ltd.

  9. The relative importance of intrinsic and extrinsic drivers to population growth vary among local populations of Greater Sage-Grouse: An integrated population modeling approach

    Science.gov (United States)

    Coates, Peter S.; Prochazka, Brian G.; Ricca, Mark A.; Halstead, Brian J.; Casazza, Michael L.; Blomberg, Erik J.; Brussee, Brianne E.; Wiechman, Lief; Tebbenkamp, Joel; Gardner, Scott C.; Reese, Kerry P.

    2018-01-01

    Consideration of ecological scale is fundamental to understanding and managing avian population growth and decline. Empirically driven models for population dynamics and demographic processes across multiple spatial scales can be powerful tools to help guide conservation actions. Integrated population models (IPMs) provide a framework for better parameter estimation by unifying multiple sources of data (e.g., count and demographic data). Hierarchical structure within such models that include random effects allow for varying degrees of data sharing across different spatiotemporal scales. We developed an IPM to investigate Greater Sage-Grouse (Centrocercus urophasianus) on the border of California and Nevada, known as the Bi-State Distinct Population Segment. Our analysis integrated 13 years of lek count data (n > 2,000) and intensive telemetry (VHF and GPS; n > 350 individuals) data across 6 subpopulations. Specifically, we identified the most parsimonious models among varying random effects and density-dependent terms for each population vital rate (e.g., nest survival). Using a joint likelihood process, we integrated the lek count data with the demographic models to estimate apparent abundance and refine vital rate parameter estimates. To investigate effects of climatic conditions, we extended the model to fit a precipitation covariate for instantaneous rate of change (r). At a metapopulation extent (i.e. Bi-State), annual population rate of change λ (er) did not favor an overall increasing or decreasing trend through the time series. However, annual changes in λ were driven by changes in precipitation (one-year lag effect). At subpopulation extents, we identified substantial variation in λ and demographic rates. One subpopulation clearly decoupled from the trend at the metapopulation extent and exhibited relatively high risk of extinction as a result of low egg fertility. These findings can inform localized, targeted management actions for specific areas

  10. Population assessment and degree of threat of chalybea Macrocarpa (Melastomataceae) endemic species from Colombia

    International Nuclear Information System (INIS)

    Gil Leguizamon, Pablo Andres; Morales Puentes, Maria Eugenia; Diaz Perez, Carlos Nelson

    2014-01-01

    Population assessment results from chalybea macrocarpaare shown, the specie is considerate ENDANGERED (EN) by its restricted area, threatened is generated by crops and extensive cattle farming. the study was conducted in the Boyaca Department (Colombia), Municipality of Arcabuco, in three established localities using herbarium and literature information; field work made possible identified distribution, density and phenology like sub criteria, allowing identify the presence extension and occupancy area. We took structural data (height, coverage and DBH) to determinate the population age's classes. Which the gathered information and the associated vegetation, the specie is re-categorized which the b IUCN criteria. It is distributed to the northwest and southern in Arcabuco, in an area of 59.9 km"2, 4 km"2 of occupancy and a population density of 50 individual/km"2. Flowering and fruiting is continuous through the year, however, most of the flowering is from March to August and fruiting from September to February. Age structure allows identified ten species between seedlings, juveniles and adults. Population is represented by few seedling individuals (10.6 %) and juveniles (20.9 %) versus adults (68.5 %). finally, C. macrocarpais upgraded to Critical Risk (CR B1ab (iii)).

  11. Construction of analytically solvable models for interacting species. [biological species competition

    Science.gov (United States)

    Rosen, G.

    1976-01-01

    The basic form of a model representation for systems of n interacting biological species is a set of essentially nonlinear autonomous ordinary differential equations. A generic canonical expression for the rate functions in the equations is reported which permits the analytical general solution to be obtained by elementary computation. It is shown that a general analytical solution is directly obtainable for models where the rate functions are prescribed by the generic canonical expression from the outset. Some illustrative examples are given which demonstrate that the generic canonical expression can be used to construct analytically solvable models for two interacting species with limit-cycle dynamics as well as for a three-species interdependence.

  12. Emergence of cytotoxic resistance in cancer cell populations: Single-cell mechanisms and population-level consequences

    International Nuclear Information System (INIS)

    Lorenzi, Tommaso; Chisholm, Rebecca H.; Lorz, Alexander; Neves de Almeida, Luís; Clairambault, Jean; Larsen, Annette K.; Escargueil, Alexandre

    2016-01-01

    We formulate an individual-based model and a population model of phenotypic evolution, under cytotoxic drugs, in a cancer cell population structured by the expression levels of survival-potential and proliferation-potential. We apply these models to a recently studied experimental system. Our results suggest that mechanisms based on fundamental laws of biology can reversibly push an actively-proliferating, and drug-sensitive, cell population to transition into a weakly-proliferative and drug-tolerant state, which will eventually facilitate the emergence of more potent, proliferating and drug-tolerant cells.

  13. Emergence of cytotoxic resistance in cancer cell populations: Single-cell mechanisms and population-level consequences

    Energy Technology Data Exchange (ETDEWEB)

    Lorenzi, Tommaso [Centre de Mathématiques et de Leurs Applications, ENS Cachan, CNRS, Cachan 94230 Cedex, France & INRIA-Paris-Rocquencourt, MAMBA Team, Domaine de Voluceau, BP105, 78153 Le Chesnay Cedex (France); Chisholm, Rebecca H. [School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052 (Australia); Lorz, Alexander; Neves de Almeida, Luís; Clairambault, Jean [Sorbonne Universités, UPMC Univ Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris (France); CNRS, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris (France); INRIA-Paris-Rocquencourt, MAMBA Team, Domaine de Voluceau, BP105, 78153 Le Chesnay Cedex (France); Larsen, Annette K.; Escargueil, Alexandre [Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris (France); INSERM, UMR-S 938, Laboratory of “Cancer Biology and Therapeutics”, F-75012, Paris (France)

    2016-06-08

    We formulate an individual-based model and a population model of phenotypic evolution, under cytotoxic drugs, in a cancer cell population structured by the expression levels of survival-potential and proliferation-potential. We apply these models to a recently studied experimental system. Our results suggest that mechanisms based on fundamental laws of biology can reversibly push an actively-proliferating, and drug-sensitive, cell population to transition into a weakly-proliferative and drug-tolerant state, which will eventually facilitate the emergence of more potent, proliferating and drug-tolerant cells.

  14. Evolutionary stellar population synthesis with MILES : I. The base models and a new line index system

    NARCIS (Netherlands)

    Vazdekis, A.; Sanchez-Blazquez, P.; Falcon-Barroso, J.; Cenarro, A. J.; Beasley, M. A.; Cardiel, N.; Gorgas, J.; Peletier, R. F.

    2010-01-01

    We present synthetic spectral energy distributions (SEDs) for single-age, single-metallicity stellar populations (SSPs) covering the full optical spectral range at moderately high resolution [full width at half-maximum (FWHM) = 2.3Å]. These SEDs constitute our base models, as they combine

  15. Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change

    Science.gov (United States)

    Maguire, Kaitlin C.; Shinneman, Douglas; Potter, Kevin M.; Hipkins, Valerie D.

    2018-01-01

    Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results

  16. Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change.

    Science.gov (United States)

    Maguire, Kaitlin C; Shinneman, Douglas J; Potter, Kevin M; Hipkins, Valerie D

    2018-03-14

    Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results

  17. Wild Plant Species with Extremely Small Populations Require Conservation and Reintroduction in China

    Science.gov (United States)

    Hai Ren; Qianmei Zhang; Hongfang Lu; Hongxiao Liu; Qinfeng Guo; Jun Wang; Shuguang Jian; Hai’ou Bao

    2012-01-01

    China is exceptionally rich in biodiversity, with more than 30000 vascular plant species that include many endemic genera, species of ancient origin, and cultivated plants (Yang et al. 2005). Because of rapid economic development, population growth, pollution, and continuing resource exploitation, China’s plant diversity faces severe threats. According to the Chinese...

  18. Monitoring of fish species in the Lamone river: distribution and morphometric measures of the populations

    Directory of Open Access Journals (Sweden)

    Riccardo Bozzi

    2010-01-01

    Full Text Available Fish samplings were carried out monthly from spring to autumn during 2008, on the Lamone river and the Campigno stream by an electrofishing, in order to verify the presence of fish populations and the most common species represented. Barb, Barbus plebejus, Blageon, Leuciscus muticellus, Chub, Leuciscus cephalus, South European Nase, Chondrostoma genei were identified. A small population of Brown trout, Salmo trutta fario was also recognized. Barb is the most represented species in all the sites. The samplings highlight that Lamone river presented conditions suitable to fully guarantee the life of the fish populations.

  19. Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

    Science.gov (United States)

    Xie, Guo-Wen; Wang, De-Lian; Yuan, Yong-Ming; Ge, Xue-Jun

    2005-04-01

    Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

  20. Ability of matrix models to explain the past and predict the future of plant populations.

    Science.gov (United States)

    McEachern, Kathryn; Crone, Elizabeth E.; Ellis, Martha M.; Morris, William F.; Stanley, Amanda; Bell, Timothy; Bierzychudek, Paulette; Ehrlen, Johan; Kaye, Thomas N.; Knight, Tiffany M.; Lesica, Peter; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F.; Ticktin, Tamara; Valverde, Teresa; Williams, Jennifer I.; Doak, Daniel F.; Ganesan, Rengaian; Thorpe, Andrea S.; Menges, Eric S.

    2013-01-01

    Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models.

  1. Ability of matrix models to explain the past and predict the future of plant populations.

    Science.gov (United States)

    Crone, Elizabeth E; Ellis, Martha M; Morris, William F; Stanley, Amanda; Bell, Timothy; Bierzychudek, Paulette; Ehrlén, Johan; Kaye, Thomas N; Knight, Tiffany M; Lesica, Peter; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F; Ticktin, Tamara; Valverde, Teresa; Williams, Jennifer L; Doak, Daniel F; Ganesan, Rengaian; McEachern, Kathyrn; Thorpe, Andrea S; Menges, Eric S

    2013-10-01

    Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models. © 2013 Society for Conservation Biology.

  2. 76 FR 77465 - Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of...

    Science.gov (United States)

    2011-12-13

    ... Population Segments of the Bearded Seal AGENCY: National Marine Fisheries Service (NMFS), National Oceanic... population segments (DPS) of the bearded seal (Erignathus barbatus) as threatened species under the... posed to this population by the projected habitat changes. Extension of Final Listing Determination The...

  3. Detection of sister-species in invasive populations of the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Uganda

    Science.gov (United States)

    Tay, Wee Tek; Walsh, Thomas K.; Kanyesigye, Dalton; Adumo, Stella; Abongosi, Joseph; Ochen, Stephen; Sserumaga, Julius; Alibu, Simon; Abalo, Grace; Asea, Godfrey; Agona, Ambrose

    2018-01-01

    The fall armyworm (FAW) Spodoptera frugiperda (J. E. Smith) is a species native to the Americas. This polyphagous lepidopteran pest was first reported in Nigeria and the Democratic Republic of São Tomé and Principe in 2016, but its presence in eastern Africa has not been confirmed via molecular characterisation. In this study, FAW specimens from western and central Uganda were identified based on the partial mtDNA COI gene sequences, with mtDNA COI haplotypes matching those identified in Nigeria and São Tomé. In this study, we sequence an additional partial mtDNA Cyt b gene and also the partial mtDNA COIII gene in Ugandan FAW samples. We detected identical mitochondrial DNA haplotypes for both the mtDNA Cyt b and COI partial genes, while combining the mtDNA COI/Cyt b haplotypes and mtDNA COIII haplotypes enabled a new maternal lineage in the Ugandan corn-preferred FAW samples to be identified. Our results suggested that the African incursions of S. frugiperda involved at least three maternal lineages. Recent full genome, phylogenetic and microsatellite analyses provided evidence to support S. frugiperda as likely consisted of two sympatric sister species known as the corn-preferred and rice-preferred strains. In our Ugandan FAW populations, we identified the presence of mtDNA haplotypes representative of both sister species. It is not known if both FAW sister species were originally introduced together or separately, and whether they have since spread as a single population. Further analyses of additional specimens originally collected from São Tomé, Nigeria and throughout Africa would be required to clarify this issue. Importantly, our finding showed that the genetic diversity of the African corn-preferred FAW species is higher than previously reported. This potentially contributed to the success of FAW establishment in Africa. Furthermore, with the additional maternal lineages detected, there is likely an increase in paternal lineages, thereby increasing

  4. Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

    Science.gov (United States)

    Maity, Hiranmay; Reddy, Govardhan

    2018-04-01

    Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

  5. An integrated modeling approach to estimating Gunnison Sage-Grouse population dynamics: combining index and demographic data.

    Science.gov (United States)

    Davis, Amy J.; Hooten, Mevin B.; Phillips, Michael L.; Doherty, Paul F.

    2014-01-01

    Evaluation of population dynamics for rare and declining species is often limited to data that are sparse and/or of poor quality. Frequently, the best data available for rare bird species are based on large-scale, population count data. These data are commonly based on sampling methods that lack consistent sampling effort, do not account for detectability, and are complicated by observer bias. For some species, short-term studies of demographic rates have been conducted as well, but the data from such studies are typically analyzed separately. To utilize the strengths and minimize the weaknesses of these two data types, we developed a novel Bayesian integrated model that links population count data and population demographic data through population growth rate (λ) for Gunnison sage-grouse (Centrocercus minimus). The long-term population index data available for Gunnison sage-grouse are annual (years 1953–2012) male lek counts. An intensive demographic study was also conducted from years 2005 to 2010. We were able to reduce the variability in expected population growth rates across time, while correcting for potential small sample size bias in the demographic data. We found the population of Gunnison sage-grouse to be variable and slightly declining over the past 16 years.

  6. Population Development of Several Species of Ants on the Cocoa Trees in South Sulawesi

    Directory of Open Access Journals (Sweden)

    Fatahuddin Fatahuddin

    2010-08-01

    Full Text Available Several species of ants with different behavior have been found in cocoa plantations and their behavior is important to be considered because it might be correlated with the degree of protection of cocoa plant from cocoa pests. The aim of this research is to manipulate and to develop ants population in environment, so they are able to establish permanently in cocoa trees. This research was conducted in Papakaju Regions Luwu Regency in Juli to November 2009. In this study, 10 cocoa trees with ants were sampled (each species of ant in 10 cocoa trees. A control of 10 tree samples without ant was also taken. In order to assess the abundance of ant population, it was grouped based on scoring, which score 1 for less than 20 ants, score 2 for 21–50 ants, score 3 for 51–200 ants, score 4 for 201–1000 ants, and score 5 for more than 1000 per tree. The results indicated that average of population score of the three ants species reached the highest population for the Oecophylla. smaragdina with average score 4.85 (>1000 ants, Dolichoderus thoracicus, with average score 3.90 (> 200 ants and Crematogaster. difformis with average score 3.10 (>200 ants. This research indicated that three species of ants, Oecophylla smaragdina (weaver ant, Dolichoderus thoracicus (cocoa black ant and Crematogaster difformis (cracking ant. in farmer cocoa plantations in South Sulawesi giving better performance against major pests of cocoa in particular cocoa pod borer (CPB. Key words: Ant Population, Oecophylla smaragdina, Dolichoderus thoracicus, Crematogaster difformis, artificial nest, cocoa.

  7. Operculina from the northwestern Pacific (Sesoko Island, Japan) Species Differentiation, Population Dynamics, Growth and Development

    Science.gov (United States)

    Woeger, Julia; Eder, Wolfgang; Kinoshita, Shunichi; Briguglio, Antonino; Hohenegger, Johann

    2017-04-01

    During the last decades larger benthic foraminifera have gained importance as indicator species and are used in a variety of applications, from ecological monitoring, studying the effects of ocean acidification, or reconstructing paleoenvironments. They significantly contribute to the carbonate budget of costal areas and are invaluable tools in biostratigraphy. Even before their advancement as bioindicators, laboratory experiments have been conducted to investigate the effects of various ecological parameters on community composition, biology of single species, or investigating the effects of salinity and temperature on stable isotope composition of the foraminiferal test, to name only a few. The natural laboratory approach (continuous sampling over a period of more than one year) was conducted at the island of Sesoko (Okinawa, Japan). in combination with µ-CT scanning was used to reveal population dynamics of 3 different morphotypes of Operculina. The clarification of reproductive cycles as well as generation and size abundances were used to calculate natural growth models. Best fit was achieved using Bertalanffy and Michaelis-Menten functions. Exponential-, logistic-, generalized logistic-, Gompertz-function yielded weaker fits, when compared by coefficient of determination as well as Akaike Information criterion. The resulting growth curves and inferred growth rates were in turn used to evaluate the quality of a laboratory cultivation experiment carried out simultaneously over a period of 15 months. Culturing parameters such as temperature, light intensities, salinity and pH and light-dark duration were continuously adapted to measurements in the field. The average investigation time in culture was 77days. 13 Individuals lived more than 200 days, 3 reproduced asexually and one sexually. 14% of 186 Individuals were lost, while 22% could not be kept alive for more than one month. Growth curves also represent an instrumental source of information for the various

  8. A probabilistic model for cell population phenotyping using HCS data.

    Directory of Open Access Journals (Sweden)

    Edouard Pauwels

    Full Text Available High Content Screening (HCS platforms allow screening living cells under a wide range of experimental conditions and give access to a whole panel of cellular responses to a specific treatment. The outcome is a series of cell population images. Within these images, the heterogeneity of cellular response to the same treatment leads to a whole range of observed values for the recorded cellular features. Consequently, it is difficult to compare and interpret experiments. Moreover, the definition of phenotypic classes at a cell population level remains an open question, although this would ease experiments analyses. In the present work, we tackle these two questions. The input of the method is a series of cell population images for which segmentation and cellular phenotype classification has already been performed. We propose a probabilistic model to represent and later compare cell populations. The model is able to fully exploit the HCS-specific information: "dependence structure of population descriptors" and "within-population variability". The experiments we carried out illustrate how our model accounts for this specific information, as well as the fact that the model benefits from considering them. We underline that these features allow richer HCS data analysis than simpler methods based on single cellular feature values averaged over each well. We validate an HCS data analysis method based on control experiments. It accounts for HCS specificities that were not taken into account by previous methods but have a sound biological meaning. Biological validation of previously unknown outputs of the method constitutes a future line of work.

  9. Evaluating population connectivity for species of conservation concern in the American Great Plains

    Science.gov (United States)

    Samuel A. Cushman; Erin L. Landguth; Curtis H. Flather

    2013-01-01

    Habitat loss and fragmentation are widely recognized as among the most important threats to global biodiversity. New analytical approaches are providing an improved ability to predict the effects of landscape change on population connectivity at vast spatial extents. This paper presents an analysis of population connectivity for three species of conservation concern [...

  10. Selection for life-history traits to maximize population growth in an invasive marine species

    DEFF Research Database (Denmark)

    Jaspers, Cornelia; Marty, Lise; Kiørboe, Thomas

    2018-01-01

    Species establishing outside their natural range, negatively impacting local ecosystems, are of increasing global concern. They often display life-history features characteristic for r-selected populations with fast growth and high reproduction rates to achieve positive population growth rates (r...

  11. Differences in the Aerobic Capacity of Flight Muscles between Butterfly Populations and Species with Dissimilar Flight Abilities

    Science.gov (United States)

    Rauhamäki, Virve; Wolfram, Joy; Jokitalo, Eija; Hanski, Ilkka; Dahlhoff, Elizabeth P.

    2014-01-01

    Habitat loss and climate change are rapidly converting natural habitats and thereby increasing the significance of dispersal capacity for vulnerable species. Flight is necessary for dispersal in many insects, and differences in dispersal capacity may reflect dissimilarities in flight muscle aerobic capacity. In a large metapopulation of the Glanville fritillary butterfly in the Åland Islands in Finland, adults disperse frequently between small local populations. Individuals found in newly established populations have higher flight metabolic rates and field-measured dispersal distances than butterflies in old populations. To assess possible differences in flight muscle aerobic capacity among Glanville fritillary populations, enzyme activities and tissue concentrations of the mitochondrial protein Cytochrome-c Oxidase (CytOx) were measured and compared with four other species of Nymphalid butterflies. Flight muscle structure and mitochondrial density were also examined in the Glanville fritillary and a long-distance migrant, the red admiral. Glanville fritillaries from new populations had significantly higher aerobic capacities than individuals from old populations. Comparing the different species, strong-flying butterfly species had higher flight muscle CytOx content and enzymatic activity than short-distance fliers, and mitochondria were larger and more numerous in the flight muscle of the red admiral than the Glanville fritillary. These results suggest that superior dispersal capacity of butterflies in new populations of the Glanville fritillary is due in part to greater aerobic capacity, though this species has a low aerobic capacity in general when compared with known strong fliers. Low aerobic capacity may limit dispersal ability of the Glanville fritillary. PMID:24416122

  12. Inequivalence of single-particle and population lifetimes in a cuprate superconductor

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Shuolong [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Sobota, J. A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Leuenberger, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); He, Y. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Hashimoto, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Lu, D. H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Eisaki, H. [National Institute of Advanced Industrial Science and Technology, Ibaraki (Japan); Kirchmann, P. S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Shen, Z. -X. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States)

    2015-06-15

    We study optimally doped Bi-2212 (Tc=96 K) using femtosecond time- and angle-resolved photoelectron spectroscopy. Energy-resolved population lifetimes are extracted and compared with single-particle lifetimes measured by equilibrium photoemission. The population lifetimes deviate from the single-particle lifetimes in the low excitation limit by 1–2 orders of magnitude. Fundamental considerations of electron scattering unveil that these two lifetimes are in general distinct, yet for systems with only electron-phonon scattering they should converge in the low-temperature, low-fluence limit. As a result, the qualitative disparity in our data, even in this limit, suggests that scattering channels beyond electron-phonon interactions play a significant role in the electron dynamics of cuprate superconductors.

  13. Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil.

    Science.gov (United States)

    Gehara, Marcelo; Garda, Adrian A; Werneck, Fernanda P; Oliveira, Eliana F; da Fonseca, Emanuel M; Camurugi, Felipe; Magalhães, Felipe de M; Lanna, Flávia M; Sites, Jack W; Marques, Ricardo; Silveira-Filho, Ricardo; São Pedro, Vinícius A; Colli, Guarino R; Costa, Gabriel C; Burbrink, Frank T

    2017-09-01

    Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data, we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest. © 2017 John Wiley & Sons Ltd.

  14. Genetic Diversity and Population Structure of Varronia curassavica: A Medicinal Polyploid Species in a Threatened Ecosystem.

    Science.gov (United States)

    Hoeltgebaum, Marcia Patricia; Dos Reis, Maurício Sedrez

    2017-06-01

    Varronia curassavica is an important medicinal species associated with the restinga, one of the most threatened coastal ecosystems of the Atlantic Forest. These circumstances call for studies aimed at estimating effective population size and gene flow to improve conservation efforts. Hence, the present study aimed to characterize the genetic diversity, ploidy level, and population structure of this species in different areas of restinga using microsatellites. Varronia curassavica was characterized as an autotetraploid, with high genetic variability, low divergence, and no significant fixation indices, indicating the absence of, or reduced, inbreeding and genetic drift in the study area. About 44% of the alleles occurred at low frequency in adults of all populations and 41% in the progenies evaluated. Gene flow was high, consistent with outcrossing species with high dispersal capacity (Nm = 4.87). The results showed no tendency toward isolation by distance. The estimated effective size indicates that the populations studied have the potential to ensure conservation of the species in the long term. The genetic variability and population structure of V. curassavica, as determined in this study, could form the foundation for activities directed toward the sustainable use of this resource and its conservation. Even though the restinga ecosystem has suffered dramatic reductions in area, this study provides evidence that this species is resilient to anthropogenic threats to its genetic integrity, since it is a polyploid with self-incompatibility mechanisms that contribute to maintaining high genetic diversity in an panmictic meta-population along the coast of Santa Catarina. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. A generic individual-based model to simulate morphogenesis, C-N acquisition and population dynamics in contrasting forage legumes.

    Science.gov (United States)

    Louarn, Gaëtan; Faverjon, Lucas

    2018-04-18

    Individual-based models (IBMs) are promising tools to disentangle plant interactions in multi-species grasslands and foster innovative species mixtures. This study describes an IBM dealing with the morphogenesis, growth and C-N acquisition of forage legumes that integrates plastic responses from functional-structural plant models. A generic model was developed to account for herbaceous legume species with contrasting above- and below-ground morphogenetic syndromes and to integrate the responses of plants to light, water and N. Through coupling with a radiative transfer model and a three-dimensional virtual soil, the model allows dynamic resolution of competition for multiple resources at individual plant level within a plant community. The behaviour of the model was assessed on a range of monospecific stands grown along gradients of light, water and N availability. The model proved able to capture the diversity of morphologies encountered among the forage legumes. The main density-dependent features known about even-age plant populations were correctly anticipated. The model predicted (1) the 'reciprocal yield' law relating average plant mass to density, (2) a self-thinning pattern close to that measured for herbaceous species and (3) consistent changes in the size structure of plant populations with time and pedo-climatic conditions. In addition, plastic changes in the partitioning of dry matter, the N acquisition mode and in the architecture of shoots and roots emerged from the integration of plant responses to their local environment. This resulted in taller plants and thinner roots when competition was dominated by light, and shorter plants with relatively more developed root systems when competition was dominated by soil resources. A population dynamic model considering growth and morphogenesis responses to multiple resources heterogeneously distributed in the environment was presented. It should allow scaling plant-plant interactions from individual to

  16. Dynamic-landscape metapopulation models predict complex response of wildlife populations to climate and landscape change

    Science.gov (United States)

    Thomas W. Bonnot; Frank R. Thompson; Joshua J. Millspaugh

    2017-01-01

    The increasing need to predict how climate change will impact wildlife species has exposed limitations in how well current approaches model important biological processes at scales at which those processes interact with climate. We used a comprehensive approach that combined recent advances in landscape and population modeling into dynamic-landscape metapopulation...

  17. Long-term species balance in sympatric populations: implications for Atlantic salmon and brown trout

    Directory of Open Access Journals (Sweden)

    Jose Luis Horreo

    2014-09-01

    Full Text Available The factors determining regional adaptation in salmonids are still unclear, but it is known that changes in their habitat imply changes in their population structure. In this preliminary study we integrate habitat data, molecular analyses (from both nuclear microsatellite and mitochondrial loci and life-history traits (measured on archaeological vertebrae and modern scales of two sympatric salmonid species: Atlantic salmon and brown trout. We propose that water temperature and geological characteristics changed the biogeographic patterns of these species through asymmetric migration and different (but complementary population growth rates. As a consequence, differences in a life-history trait (mean number of years at sea and population sizes were detected between regions, suggesting a process of substitution of Atlantic salmon by brown trout.

  18. Integrative demographic modeling reveals population level impacts of PCB toxicity to juvenile snapping turtles

    International Nuclear Information System (INIS)

    Salice, Christopher J.; Rowe, Christopher L.; Eisenreich, Karen M.

    2014-01-01

    A significant challenge in ecotoxicology and risk assessment lies in placing observed contaminant effects in a meaningful ecological context. Polychlorinated biphenyls (PCBs) have been shown to affect juvenile snapping turtle survival and growth but the ecological significance of these effects is difficult to discern without a formal, population-level assessment. We used a demographic matrix model to explore the potential population-level effects of PCBs on turtles. Our model showed that effects of PCBs on juvenile survival, growth and size at hatching could translate to negative effects at the population level despite the fact that these life cycle components do not typically contribute strongly to population level processes. This research points to the utility of using integrative demographic modeling approaches to better understand contaminant effects in wildlife. The results indicate that population-level effects are only evident after several years, suggesting that for long-lived species, detecting adverse contaminant effects could prove challenging. -- Highlights: • Previous studies have shown the PCBs can impact juvenile snapping turtles. • We used a demographic model of turtles to evaluate population-level PCB effects. • PCB effects on turtles may translate to negative population responses. • Long-term monitoring is needed to detect contaminant effects on natural turtle populations. • Demographic models can improve our understanding contaminant ecotoxicity. -- A demographic model was used to show that PCB induced effects on young snapping turtles can result in adverse effects at the population level

  19. Using matrix population models to inform biological control management of the wheat stem sawfly, Cephus cinctus

    Science.gov (United States)

    Demographic models are a powerful means of identifying vulnerable life stages of pest species and assessing the potential effectiveness of various management approaches in reducing pest population growth and spread. In a biological control context, such models can be used to focus foreign explorati...

  20. Phytoplankton IF-FISH: Species-specific labeling of cellular proteins by immunofluorescence (IF) with simultaneous species identification by fluorescence immunohybridization (FISH).

    Science.gov (United States)

    Meek, Megan E; Van Dolah, Frances M

    2016-05-01

    Phytoplankton rarely occur as unialgal populations. Therefore, to study species-specific protein expression, indicative of physiological status in natural populations, methods are needed that will both assay for a protein of interest and identify the species expressing it. Here we describe a protocol for IF-FISH, a dual labeling procedure using immunofluorescence (IF) labeling of a protein of interest followed by fluorescence in situ hybridization (FISH) to identify the species expressing that protein. The protocol was developed to monitor expression of the cell cycle marker proliferating cell nuclear antigen (PCNA) in the red tide dinoflagellate, Karenia brevis, using a large subunit (LSU) rRNA probe to identify K. brevis in a mixed population of morphologically similar Karenia species. We present this protocol as proof of concept that IF-FISH can be successfully applied to phytoplankton cells. This method is widely applicable for the analysis of single-cell protein expression of any protein of interest within phytoplankton communities. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. 76 FR 14883 - Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of...

    Science.gov (United States)

    2011-03-18

    ...-XZ58 Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of..., published a proposed rule to list the Beringia and Okhotsk Distinct Population Segments (DPSs) of the... published a proposed rule to list the Beringia and Okhotsk Distinct Population Segments (DPSs) of the...

  2. The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago

    Directory of Open Access Journals (Sweden)

    Giles Jenny

    2009-02-01

    Full Text Available Abstract Background The territorial fishing zones of Australia and Indonesia are contiguous to the north of Australia in the Timor and Arafura Seas and in the Indian Ocean to the north of Christmas Island. The area surrounding the shared boundary consists of a variety of bio-diverse marine habitats including shallow continental shelf waters, oceanic trenches and numerous offshore islands. Both countries exploit a variety of fisheries species, including whaler (Carcharhinus spp. and hammerhead sharks (Sphyrna spp.. Despite their differences in social and financial arrangements, the two countries are motivated to develop complementary co-management practices to achieve resource sustainability. An essential starting point is knowledge of the degree of population subdivision, and hence fisheries stock status, in exploited species. Results Populations of four commercially harvested shark species (Carcharhinus obscurus, Carcharhinus sorrah, Prionace glauca, Sphyrna lewini were sampled from northern Australia and central Indonesia. Neutral genetic markers (mitochondrial DNA control region sequence and allelic variation at co-dominant microsatellite loci revealed genetic subdivision between Australian and Indonesian populations of C. sorrah. Further research is needed to address the possibility of genetic subdivision among C. obscurus populations. There was no evidence of genetic subdivision for P. glauca and S. lewini populations, but the sampling represented a relatively small part of their distributional range. For these species, more detailed analyses of population genetic structure is recommended in the future. Conclusion Cooperative management between Australia and Indonesia is the best option at present for P. glauca and S. lewini, while C. sorrah and C. obscurus should be managed independently. On-going research on these and other exploited shark and ray species is strongly recommended. Biological and ecological similarity between species may

  3. Infection, Reproduction Potential, and Root Galling by Root-knot Nematode Species and Concomitant Populations on Peanut and Tobacco

    Science.gov (United States)

    Hirunsalee, Anan; Barker, K. R.; Beute, M. K.

    1995-01-01

    Single populations of Meloidogyne arenaria races 1 (MA1) and 2 (MA2) and M. hapla (MH), and mixed populations of MA1 + MA2 and MA1 + MH with four inoculum levels of eggs were tested on peanut cv. 'Florigiant' and M. incognita-resistant tobacco cv. 'McNair 373' in a greenhouse experiment. Root infection, female development, and reproduction of MA2 on peanut and MA1 on resistant tobacco were limited at 2 and 6 weeks. MA1, MH, and MA1 + MH on peanut had similar root infection (total parasitic forms per root unit) at both 2 and 6 weeks, and similar female development and reproduction potentials at 6 weeks. MA2 tended to depress root infection, female development, and reproduction of MA1 on peanut. MH had little effect on MA1 on this crop. On tobacco, MA2 population had greater incidence of root infection than did MH at 2 weeks. The two nematode species had similar development in roots at 6 weeks. All of these processes were restricted when either MA2 or MH was present together with MA1. As initial inoculum level of parasitically fit populations increased, relative infection ratio on both peanut and tobacco, and reproduction factor on peanut decreased. Populations that had high infection incidence and reproduction rates induced greater root galling than did other populations. Root galling was suppressed in the presence of antagonistic response between nematode populations. PMID:19277277

  4. Inferring the demographic history of European Ficedula flycatcher populations

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    Backström Niclas

    2013-01-01

    Full Text Available Abstract Background Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of Conclusions Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.

  5. Population Genetics of the Endemic Hawaiian Species Chrysodracon hawaiiensis and Chrysodracon auwahiensis (Asparagaceae: Insights from RAPD and ISSR Variation

    Directory of Open Access Journals (Sweden)

    Pei-Luen Lu

    2016-08-01

    Full Text Available The genus Chrysodracon has six endemic species in the Hawaii Islands. Chrysodracon hawaiiensis is endemic to Hawaii Island and was described as a distinct species in 1980. It was listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources (IUCN Red List in 1997. This woody plant species was, at one time, common in exposed dry forests, but it became very rare due to grazing pressure and human development. The tree species Chrysodracon auwahiensis (C. auwahiensis, endemic to Maui and Molokai, still has large adult populations in dry lands of the islands, but unfortunately no regeneration from seed has been reported in those areas for many years. The two endemic species were examined using the molecular technique of random amplified polymorphic DNA (RAPD and inter simple sequence repeats (ISSR to determine the genetic structure of the populations and the amount of variation. Both species possess similar genetic structure. Larger and smaller populations of both species contain similar levels of genetic diversity as determined by the number of polymorphic loci, estimated heterozygosity, and Shannon’s index of genetic diversity. Although population diversity of Chrysodracon hawaiiensis (C. hawaiiensis is thought to have remained near pre-disturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Conservation recommendations for both species are suggested.

  6. Plastic responses to elevated temperature in low and high elevation populations of three grassland species.

    Science.gov (United States)

    Frei, Esther R; Ghazoul, Jaboury; Pluess, Andrea R

    2014-01-01

    Local persistence of plant species in the face of climate change is largely mediated by genetic adaptation and phenotypic plasticity. In species with a wide altitudinal range, population responses to global warming are likely to differ at contrasting elevations. In controlled climate chambers, we investigated the responses of low and high elevation populations (1200 and 1800 m a.s.l.) of three nutrient-poor grassland species, Trifolium montanum, Ranunculus bulbosus, and Briza media, to ambient and elevated temperature. We measured growth-related, reproductive and phenological traits, evaluated differences in trait plasticity and examined whether trait values or plasticities were positively related to approximate fitness and thus under selection. Elevated temperature induced plastic responses in several growth-related traits of all three species. Although flowering phenology was advanced in T. montanum and R. bulbosus, number of flowers and reproductive allocation were not increased under elevated temperature. Plasticity differed between low and high elevation populations only in leaf traits of T. montanum and B. media. Some growth-related and phenological traits were under selection. Moreover, plasticities were not correlated with approximate fitness indicating selectively neutral plastic responses to elevated temperature. The observed plasticity in growth-related and phenological traits, albeit variable among species, suggests that plasticity is an important mechanism in mediating plant responses to elevated temperature. However, the capacity of species to respond to climate change through phenotypic plasticity is limited suggesting that the species additionally need evolutionary adaptation to adjust to climate change. The observed selection on several growth-related and phenological traits indicates that the study species have the potential for future evolution in the context of a warming climate.

  7. Spatial structures in a simple model of population dynamics for parasite-host interactions

    Energy Technology Data Exchange (ETDEWEB)

    Dong, J. J.; Skinner, B.; Breecher, N.; Schmittmann, B.; Zia, R. K. P.

    2015-08-01

    Spatial patterning can be crucially important for understanding the behavior of interacting populations. Here we investigate a simple model of parasite and host populations in which parasites are random walkers that must come into contact with a host in order to reproduce. We focus on the spatial arrangement of parasites around a single host, and we derive using analytics and numerical simulations the necessary conditions placed on the parasite fecundity and lifetime for the populations long-term survival. We also show that the parasite population can be pushed to extinction by a large drift velocity, but, counterintuitively, a small drift velocity generally increases the parasite population.

  8. Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd.

    Science.gov (United States)

    Peng, Yan Qun; Fan, Ling Ling; Mao, Fu Ying; Zhao, Yun Sheng; Xu, Rui; Yin, Yu Jie; Chen, Xin; Wan, De Guang; Zhang, Xin Hui

    2018-03-01

    Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL)=84.2%, Nei's gene diversity (h)=0.3296 and Shannon's information index (I)=0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL=81.9%, h=0.3154, I=0.4635) showed a higher genetic diversity level than the cultivated population (PPL=63.9%, h=0.2507, I=0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  9. Setting population targets for mammals using body mass as a predictor of population persistence.

    Science.gov (United States)

    Hilbers, Jelle P; Santini, Luca; Visconti, Piero; Schipper, Aafke M; Pinto, Cecilia; Rondinini, Carlo; Huijbregts, Mark A J

    2017-04-01

    Conservation planning and biodiversity assessments need quantitative targets to optimize planning options and assess the adequacy of current species protection. However, targets aiming at persistence require population-specific data, which limit their use in favor of fixed and nonspecific targets, likely leading to unequal distribution of conservation efforts among species. We devised a method to derive equitable population targets; that is, quantitative targets of population size that ensure equal probabilities of persistence across a set of species and that can be easily inferred from species-specific traits. In our method, we used models of population dynamics across a range of life-history traits related to species' body mass to estimate minimum viable population targets. We applied our method to a range of body masses of mammals, from 2 g to 3825 kg. The minimum viable population targets decreased asymptotically with increasing body mass and were on the same order of magnitude as minimum viable population estimates from species- and context-specific studies. Our approach provides a compromise between pragmatic, nonspecific population targets and detailed context-specific estimates of population viability for which only limited data are available. It enables a first estimation of species-specific population targets based on a readily available trait and thus allows setting equitable targets for population persistence in large-scale and multispecies conservation assessments and planning. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

  10. Modelling interactions of toxicants and density dependence in wildlife populations

    Science.gov (United States)

    Schipper, Aafke M.; Hendriks, Harrie W.M.; Kauffman, Matthew J.; Hendriks, A. Jan; Huijbregts, Mark A.J.

    2013-01-01

    1. A major challenge in the conservation of threatened and endangered species is to predict population decline and design appropriate recovery measures. However, anthropogenic impacts on wildlife populations are notoriously difficult to predict due to potentially nonlinear responses and interactions with natural ecological processes like density dependence. 2. Here, we incorporated both density dependence and anthropogenic stressors in a stage-based matrix population model and parameterized it for a density-dependent population of peregrine falcons Falco peregrinus exposed to two anthropogenic toxicants [dichlorodiphenyldichloroethylene (DDE) and polybrominated diphenyl ethers (PBDEs)]. Log-logistic exposure–response relationships were used to translate toxicant concentrations in peregrine falcon eggs to effects on fecundity. Density dependence was modelled as the probability of a nonbreeding bird acquiring a breeding territory as a function of the current number of breeders. 3. The equilibrium size of the population, as represented by the number of breeders, responded nonlinearly to increasing toxicant concentrations, showing a gradual decrease followed by a relatively steep decline. Initially, toxicant-induced reductions in population size were mitigated by an alleviation of the density limitation, that is, an increasing probability of territory acquisition. Once population density was no longer limiting, the toxicant impacts were no longer buffered by an increasing proportion of nonbreeders shifting to the breeding stage, resulting in a strong decrease in the equilibrium number of breeders. 4. Median critical exposure concentrations, that is, median toxicant concentrations in eggs corresponding with an equilibrium population size of zero, were 33 and 46 μg g−1 fresh weight for DDE and PBDEs, respectively. 5. Synthesis and applications. Our modelling results showed that particular life stages of a density-limited population may be relatively insensitive to

  11. New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

    Science.gov (United States)

    Doyle, Jacqueline M.; Bell, Douglas A.; Bloom, Peter H.; Emmons, Gavin; Fesnock, Amy; Katzner, Todd; LePre, Larry; Leonard, Kolbe; SanMiguel, Phillip; Westerman, Rick; DeWoody, J. Andrew

    2018-01-01

    BackgroundManagement requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.ResultsWe sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.ConclusionsOur study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating

  12. When is a species declining? Optimizing survey effort to detect population changes in reptiles.

    Directory of Open Access Journals (Sweden)

    David Sewell

    Full Text Available Biodiversity monitoring programs need to be designed so that population changes can be detected reliably. This can be problematical for species that are cryptic and have imperfect detection. We used occupancy modeling and power analysis to optimize the survey design for reptile monitoring programs in the UK. Surveys were carried out six times a year in 2009-2010 at multiple sites. Four out of the six species--grass snake, adder, common lizard, slow-worm -were encountered during every survey from March-September. The exceptions were the two rarest species--sand lizard and smooth snake--which were not encountered in July 2009 and March 2010 respectively. The most frequently encountered and most easily detected species was the slow-worm. For the four widespread reptile species in the UK, three to four survey visits that used a combination of directed transect walks and artificial cover objects resulted in 95% certainty that a species would be detected if present. Using artificial cover objects was an effective detection method for most species, considerably increased the detection rate of some, and reduced misidentifications. To achieve an 85% power to detect a decline in any of the four widespread species when the true decline is 15%, three surveys at a total of 886 sampling sites, or four surveys at a total of 688 sites would be required. The sampling effort needed reduces to 212 sites surveyed three times, or 167 sites surveyed four times, if the target is to detect a true decline of 30% with the same power. The results obtained can be used to refine reptile survey protocols in the UK and elsewhere. On a wider scale, the occupancy study design approach can be used to optimize survey effort and help set targets for conservation outcomes for regional or national biodiversity assessments.

  13. Population FBA predicts metabolic phenotypes in yeast.

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    Piyush Labhsetwar

    2017-09-01

    Full Text Available Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media. We find the partitioning of flux between fermentation and respiration predicted by our model agrees with recent 13C fluxomics experiments, and that our model largely recovers the Crabtree effect (the experimentally known bias among certain yeast species toward fermentation with the production of ethanol even in the presence of oxygen, while FBA without proteomics constraints predicts respirative metabolism almost exclusively. The comparisons to the 13C study showed improvement upon inclusion of the correlations and motivated a technique to systematically identify inconsistent kinetic parameters in the literature. The minor secretion fluxes for glycerol and acetate are underestimated by our method, which indicate a need for further refinements to the metabolic model. For yeast cells grown in synthetic defined (SD medium, the calculated broad distribution of growth rates matches experimental observations from single cell studies, and we characterize several metabolic phenotypes within our modeled populations that make use of diverse pathways. Fast growing yeast cells are predicted to perform significant amount of respiration, use serine-glycine cycle and produce ethanol in mitochondria as opposed to slow growing cells. We use a genetic algorithm to determine the proteomics constraints necessary to reproduce the growth rate distributions seen experimentally. We find that a core set of 51 constraints are essential but

  14. A REVIEW OF SINGLE SPECIES TOXICITY TESTS: ARE THE TESTS RELIABLE PREDICTORS OF AQUATIC ECOSYSTEM COMMUNITY RESPONSES?

    Science.gov (United States)

    This document provides a comprehensive review to evaluate the reliability of indicator species toxicity test results in predicting aquatic ecosystem impacts, also called the ecological relevance of laboratory single species toxicity tests.

  15. Tackling Biocomplexity with Meta-models for Species Risk Assessment

    Directory of Open Access Journals (Sweden)

    Philip J. Nyhus

    2007-06-01

    Full Text Available We describe results of a multi-year effort to strengthen consideration of the human dimension into endangered species risk assessments and to strengthen research capacity to understand biodiversity risk assessment in the context of coupled human-natural systems. A core group of social and biological scientists have worked with a network of more than 50 individuals from four countries to develop a conceptual framework illustrating how human-mediated processes influence biological systems and to develop tools to gather, translate, and incorporate these data into existing simulation models. A central theme of our research focused on (1 the difficulties often encountered in identifying and securing diverse bodies of expertise and information that is necessary to adequately address complex species conservation issues; and (2 the development of quantitative simulation modeling tools that could explicitly link these datasets as a way to gain deeper insight into these issues. To address these important challenges, we promote a "meta-modeling" approach where computational links are constructed between discipline-specific models already in existence. In this approach, each model can function as a powerful stand-alone program, but interaction between applications is achieved by passing data structures describing the state of the system between programs. As one example of this concept, an integrated meta-model of wildlife disease and population biology is described. A goal of this effort is to improve science-based capabilities for decision making by scientists, natural resource managers, and policy makers addressing environmental problems in general, and focusing on biodiversity risk assessment in particular.

  16. Detection of four important Eimeria species by multiplex PCR in a single assay.

    Science.gov (United States)

    You, Myung-Jo

    2014-06-01

    The oocysts of some of the recognized species of chicken coccidiosis are difficult to distinguish morphologically. Diagnostic laboratories are increasingly utilizing DNA-based technologies for the specific identification of Eimeria species. This study reports a multiplex polymerase chain reaction (PCR) assay based on internal transcribed spacer-1 (ITS-1) for the simultaneous diagnosis of the Eimeria tenella, Eimeria acervulina, Eimeria maxima, and Eimeria necatrix species, which infect domestic fowl. Primer pairs specific to each species were designed in order to generate a ladder of amplification products ranging from 20 to 25 bp, and a common optimum annealing temperature for these species was determined to be 52.5 °C. Sensitivity tests were performed for each species, showing a detection threshold of 1-5 pg. All the species were amplified homogeneously, and a homogenous band ladder was observed, indicating that the assay permitted the simultaneous detection of all the species in a single-tube reaction. In the phylogenic study, there was a clear species clustering, which was irrespective of geographical location, for all the ITS-1 sequences used. This multiplex PCR assay represents a rapid and potential cost-effective diagnostic method for the detection of some key Eimeria species that infect domestic fowl. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  17. Response of different populations of seven lady beetle species to lambda-cyhalothrin with record of resistance.

    Science.gov (United States)

    Rodrigues, Agna R S; Spindola, Aline F; Torres, Jorge B; Siqueira, Herbert A A; Colares, Felipe

    2013-10-01

    Simultaneous use of biological and chemical controls is a valued and historic goal of integrated pest management, but has rarely been achieved. One explanation for this failure may be the inadequate documentation of field populations of natural enemies for insecticide tolerance or resistance because natural enemies surviving insecticide application do not create problems like resistant pest species. Therefore, this study investigated 31 populations of lady beetles (Coleoptera: Coccinellidae) regarding their susceptibility to lambda-cyhalothrin, a pyrethroid insecticide that is widely used in cotton and other crops to control lepidopteran and coleopteran pests that are not targeted as prey by lady beetles. The study focused on seven coccinellid species common in cotton fields Coleomegilla maculata De Geer, Cycloneda sanguinea (L.), Eriopis connexa Germar, Harmonia axyridis (Pallas), Hippodamia convergens Guérin-Méneville, Olla v-nigrum (Mulsant), and Brumoides foudrasi (Mulsant) and one lady beetle species [Curinus coeruleus Mulsant] from a non-cotton ecosystem for comparisons. Dose-mortality curves were estimated after topical treatment of adult lady beetles with lambda-cyhalothrin. Statistically significant variations in lady beetle susceptibility were observed between species and between populations of a given species. Seven and eighteen populations of lady beetles exhibited greater values of LD50 and LD90, respectively, than the highest recommended field rate of lambda-cyhalothrin (20g a.i./hectare≈0.2g a.i./L) for cotton fields in Brazil. Furthermore, based on LD50 values, 29 out of 30 tested populations of lady beetles exhibited ratios of relative tolerance varying from 2- to 215-fold compared to the toxicity of lambda-cyhalothrin to the boll weevil, Anthonomus grandis Boh. (Coleoptera: Curculionidae). Four populations of E. connexa were 10.5-37.7 times more tolerant than the most susceptible population and thus were considered to be resistant to lambda

  18. Population dynamics and population control of Galium aparine L.

    NARCIS (Netherlands)

    Weide, van der R.Y.

    1993-01-01

    The population biology of Galium aparine L. needs to be better understood, in order to be able to rationalize decisions about the short- and long-term control of this weed species for different cropping practices.

    A population dynamics model was developed to

  19. Change Points in the Population Trends of Aerial-Insectivorous Birds in North America: Synchronized in Time across Species and Regions.

    Directory of Open Access Journals (Sweden)

    Adam C Smith

    Full Text Available North American populations of aerial insectivorous birds are in steep decline. Aerial insectivores (AI are a group of bird species that feed almost exclusively on insects in flight, and include swallows, swifts, nightjars, and flycatchers. The causes of the declines are not well understood. Indeed, it is not clear when the declines began, or whether the declines are shared across all species in the group (e.g., caused by changes in flying insect populations or specific to each species (e.g., caused by changes in species' breeding habitat. A recent study suggested that population trends of aerial insectivores changed for the worse in the 1980s. If there was such a change point in trends of the group, understanding its timing and geographic pattern could help identify potential causes of the decline. We used a hierarchical Bayesian, penalized regression spline, change point model to estimate group-level change points in the trends of 22 species of AI, across 153 geographic strata of North America. We found evidence for group-level change points in 85% of the strata. Change points for flycatchers (FC were distinct from those for swallows, swifts and nightjars (SSN across North America, except in the Northeast, where all AI shared the same group-level change points. During the 1980s, there was a negative change point across most of North America, in the trends of SSN. For FC, the group-level change points were more geographically variable, and in many regions there were two: a positive change point followed by a negative change point. This group-level synchrony in AI population trends is likely evidence of a response to a common environmental factor(s with similar effects on many species across broad spatial extents. The timing and geographic patterns of the change points that we identify here should provide a spring-board for research into the causes behind aerial insectivore declines.

  20. Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers.

    Science.gov (United States)

    Hilmarsson, Hrannar Smári; Hytönen, Timo; Isobe, Sachiko; Göransson, Magnus; Toivainen, Tuomas; Hallsson, Jón Hallsteinn

    2017-01-01

    The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.

  1. Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Hrannar Smári Hilmarsson

    Full Text Available The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.

  2. Land use as a Driver of Patterns of Rodenticide Exposure in Modeled Kit Fox Populations

    Science.gov (United States)

    Although rodenticides are increasingly regulated, they nonetheless cause poisonings in many non-target wildlife species. Second-generation anticoagualant rodenticide use is common in agricultural and residential lands. Here, we use an individual-based population model to assess t...

  3. Single-tier city logistics model for single product

    Science.gov (United States)

    Saragih, N. I.; Nur Bahagia, S.; Suprayogi; Syabri, I.

    2017-11-01

    This research develops single-tier city logistics model which consists of suppliers, UCCs, and retailers. The problem that will be answered in this research is how to determine the location of UCCs, to allocate retailers to opened UCCs, to assign suppliers to opened UCCs, to control inventory in the three entities involved, and to determine the route of the vehicles from opened UCCs to retailers. This model has never been developed before. All the decisions will be simultaneously optimized. Characteristic of the demand is probabilistic following a normal distribution, and the number of product is single.

  4. Habitat shift in invading species: Zebra and quagga mussel population characteristics on shallow soft substrates

    Science.gov (United States)

    Berkman, P.A.; Garton, D.W.; Haltuch, M.A.; Kennedy, G.W.; Febo, L.R.

    2000-01-01

    Unexpected habitat innovations among invading species are illustrated by the expansion of dreissenid mussels across sedimentary environments in shallow water unlike the hard substrates where they are conventionally known. In this note, records of population characteristics of invading zebra (Dreissena polymorpha) and quagga (Dreissena bugensis) mussels from 1994 through 1998 are reported from shallow (less than 20 m) sedimentary habitats in western Lake Erie. Haphazard SCUBA collections of these invading species indicated that combined densities of zebra and quagga mussels ranged from 0 to 32,500 individuals per square meter between 1994 and 1998, with D. polymorpha comprising 75-100% of the assemblages. These mixed mussel populations, which were attached by byssal threads to each other and underlying sand-grain sediments, had size-frequency distributions that were typical of colonizing populations on hard substrates. Moreover, the presence of two mussel cohorts within the 1994 samples indicated that these species began expanding onto soft substrates not later than 1992, within 4 years of their initial invasion in western Lake Erie. Such historical data provide baselines for interpreting adaptive innovations, ecological interactions and habitat shifts among the two invading dreissenid mussel species in North America.

  5. Modeling the Potential Distribution of Picea chihuahuana Martínez, an Endangered Species at the Sierra Madre Occidental, Mexico

    Directory of Open Access Journals (Sweden)

    Victor Aguilar-Soto

    2015-03-01

    Full Text Available Species distribution models (SDMs help identify areas for the development of populations or communities to prevent extinctions, especially in the face of the global environmental change. This study modeled the potential distribution of the tree Picea chihuahuana Martínez, a species in danger of extinction, using the maximum entropy modeling method (MaxEnt at three scales: local, state and national. We used a total of 38 presence data from the Sierra Madre Occidental. At the local scale, we compared MaxEnt with the reclassification and overlay method integrated in a geographic information system. MaxEnt generated maps with a high predictive capability (AUC > 0.97. The distribution of P. chihuahuana is defined by vegetation type and minimum temperature at national and state scales. At the local scale, both models calculated similar areas for the potential distribution of the species; the variables that better defined the species distribution were vegetation type, aspect and distance to water flows. Populations of P. chihuahuana have always been small, but our results show potential habitat greater than the area of the actual distribution. These results provide an insight into the availability of areas suitable for the species’ regeneration, possibly through assisted colonization.

  6. Temporal correlations in population trends: Conservation implications from time-series analysis of diverse animal taxa

    Science.gov (United States)

    David Keith; H. Resit Akcakaya; Stuart H.M. Butchart; Ben Collen; Nicholas K. Dulvy; Elizabeth E. Holmes; Jeffrey A. Hutchings; Doug Keinath; Michael K. Schwartz; Andrew O. Shelton; Robin S. Waples

    2015-01-01

    Population trends play a large role in species risk assessments and conservation planning, and species are often considered threatened if their recent rate of decline meets certain thresholds, regardless how large the population is. But how reliable an indicator of extinction risk is a single estimate of population trend? Given the integral role this decline-...

  7. Redescription of the Advertisement Call of Five Species of Thoropa (Anura, Cycloramphidae), Including Recordings of Rare and Endangered Species.

    Science.gov (United States)

    Nunes-de-Almeida, Carlos H L; Assis, Clodoaldo L; Feio, Renato N; Toledo, Luís Felipe

    2016-01-01

    Frogs of the genus Thoropa comprise six endemic Brazilian species on the Eastern side of the country. Little is known about their natural history, especially about their acoustic communication. Therefore, aiming to provide an overview of their vocalizations, we analyzed and redescribed male advertisement calls of three living and two possibly extinct species. The smaller species, T. petropolitana and T. lutzi, produce simple calls (one single note) with a higher frequency range than the remaining larger ones. On the other hand, the larger species present complex calls, with more than one note: T. megatympanum calls have three notes, T. taophora calls have four notes, and T. miliaris calls varies from three to six notes. Population snout-vent length negatively correlated with peak of dominant frequency as expected. However, highlighted differences between two populations of T. lutzi, which could indicate need of further taxonomic evaluation of those lineages. Peculiar morphology, such as the absence of vocal sacs and slits, may have contributed to their call variation and highly banded frequency structure. If the observed population differences reflect species-level differences, T. lutzi may be classified as a critically endangered species, as T. petropolitana. Furthermore, we provided a suggestion to an unusual behavior in frogs: calling with the mouth open in the smaller species of the genus.

  8. Population Diversity and Dispersal of Two Species of Stoneflies (Order Plecoptera) Within Four Watersheds of Northeastern Ohio.

    Science.gov (United States)

    Yasick, A. L.; Wolin, J. A.; Krebs, R. A.

    2005-05-01

    This study investigates two species of stoneflies with potentially opposing dispersal capabilities and genetic structure within four watersheds in the Lake Erie drainage system of Northeast Ohio. This research is two fold; it provides information on genetic variation of two understudied aquatic invertebrate species and the impact of human land-use practices on this variation. Populations of Allocapnia recta, a winter emerging stonefly are predicted to have the least genetic variation within the four watersheds and most differences among sites due to its rudimentary wing structure and winter emergence. Leuctra tenuis is predicted to have greater genetic variability within sites and fewer differences among sites because of its higher migration potential. In both species, models of isolation by distance will be tested. Distinct polymorphisms exist within the 16s rRNA region of A. recta suggesting that this fragment has sufficient variation to address these questions.

  9. Variation in the local population dynamics of the short-lived Opuntia macrorhiza (Cactaceae).

    Science.gov (United States)

    Haridas, C V; Keeler, Kathleen H; Tenhumberg, Brigitte

    2015-03-01

    Spatiotemporal variation in demographic rates can have profound effects for population persistence, especially for dispersal-limited species living in fragmented landscapes. Long-term studies of plants in such habitats help with understanding the impacts of fragmentation on population persistence but such studies are rare. In this work, we reanalyzed demographic data from seven years of the short-lived cactus Opuntia macrorhiza var. macrorhiza at five plots in Boulder, Colorado. Previous work combining data from all years and all plots predicted a stable population (deterministic log lamda approximately 0). This approach assumed that all five plots were part of a single population. Since the plots were located in a suburban-agricultural interface separated by highways, grazing lands, and other barriers, and O. macrorhiza is likely dispersal limited, we analyzed the dynamics of each plot separately using stochastic matrix models assuming each plot represented a separate population. We found that the stochastic population growth rate log lamdaS varied widely between populations (log lamdaS = 0.1497, 0.0774, -0.0230, -0.2576, -0.4989). The three populations with the highest growth rates were located close together in space, while the two most isolated populations had the lowest growth rates suggesting that dispersal between populations is critical for the population viability of O. macrorhiza. With one exception, both our prospective (stochastic elasticity) and retrospective (stochastic life table response experiments) analysis suggested that means of stasis and growth, especially of smaller plants, were most important for population growth rate. This is surprising because recruitment is typically the most important vital rate in a short-lived species such as O. macrorhiza. We found that elasticity to the variance was mostly negligible, suggesting that O. macrorhiza populations are buffered against large temporal variation. Finally, single-year elasticities to means

  10. Discrete bivariate population balance modelling of heteroaggregation processes.

    Science.gov (United States)

    Rollié, Sascha; Briesen, Heiko; Sundmacher, Kai

    2009-08-15

    Heteroaggregation in binary particle mixtures was simulated with a discrete population balance model in terms of two internal coordinates describing the particle properties. The considered particle species are of different size and zeta-potential. Property space is reduced with a semi-heuristic approach to enable an efficient solution. Aggregation rates are based on deterministic models for Brownian motion and stability, under consideration of DLVO interaction potentials. A charge-balance kernel is presented, relating the electrostatic surface potential to the property space by a simple charge balance. Parameter sensitivity with respect to the fractal dimension, aggregate size, hydrodynamic correction, ionic strength and absolute particle concentration was assessed. Results were compared to simulations with the literature kernel based on geometric coverage effects for clusters with heterogeneous surface properties. In both cases electrostatic phenomena, which dominate the aggregation process, show identical trends: impeded cluster-cluster aggregation at low particle mixing ratio (1:1), restabilisation at high mixing ratios (100:1) and formation of complex clusters for intermediate ratios (10:1). The particle mixing ratio controls the surface coverage extent of the larger particle species. Simulation results are compared to experimental flow cytometric data and show very satisfactory agreement.

  11. Understanding and estimating effective population size for practical application in marine species management.

    Science.gov (United States)

    Hare, Matthew P; Nunney, Leonard; Schwartz, Michael K; Ruzzante, Daniel E; Burford, Martha; Waples, Robin S; Ruegg, Kristen; Palstra, Friso

    2011-06-01

    Effective population size (N(e)) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of N(e) is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population's current and future viability. Nevertheless, compared with ecological and demographic parameters, N(e) has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved N(e) estimation; however, some obstacles remain for the practical application of N(e) estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of N(e) over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary N(e) estimates and suggest that different sampling designs can be combined to compare largely independent measures of N(e) for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary N(e) and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating N(e) by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating N(e) estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in N(e) from hatchery-based population

  12. Invasive rats on tropical islands: Their population biology and impacts on native species

    Directory of Open Access Journals (Sweden)

    Grant A. Harper

    2015-01-01

    Full Text Available The three most invasive rat species, black or ship rat Rattus rattus, brown or Norway rats, R. norvegicus and Pacific rat, R. exulans have been incrementally introduced to islands as humans have explored the world’s oceans. They have caused serious deleterious effects through predation and competition, and extinction of many species on tropical islands, many of which are biodiversity hotspots. All three rat species are found in virtually all habitat types, including mangrove and arid shrub land. Black rats tend to dominate the literature but despite this the population biology of invasive rats, particularly Norway rats, is poorly researched on tropical islands. Pacific rats can often exceed population densities of well over 100 rats ha−1 and black rats can attain densities of 119 rats ha−1, which is much higher than recorded on most temperate islands. High densities are possibly due to high recruitment of young although the data to support this are limited. The generally aseasonally warm climate can lead to year-round breeding but can be restricted by either density-dependent effects interacting with resource constraints often due to aridity. Apparent adverse impacts on birds have been well recorded and almost all tropical seabirds and land birds can be affected by rats. On the Pacific islands, black rats have added to declines and extinctions of land birds caused initially by Pacific rats. Rats have likely caused unrecorded extinctions of native species on tropical islands. Further research required on invasive rats on tropical islands includes the drivers of population growth and carrying capacities that result in high densities and how these differ to temperate islands, habitat use of rats in tropical vegetation types and interactions with other tropical species, particularly the reptiles and invertebrates, including crustaceans.

  13. Extracting Models in Single Molecule Experiments

    Science.gov (United States)

    Presse, Steve

    2013-03-01

    Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

  14. Projecting future expansion of invasive species: comparing and improving methodologies for species distribution modeling.

    Science.gov (United States)

    Mainali, Kumar P; Warren, Dan L; Dhileepan, Kunjithapatham; McConnachie, Andrew; Strathie, Lorraine; Hassan, Gul; Karki, Debendra; Shrestha, Bharat B; Parmesan, Camille

    2015-12-01

    Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships for Parthenium hysterophorus L. (Asteraceae) with four modeling methods run with multiple scenarios of (i) sources of occurrences and geographically isolated background ranges for absences, (ii) approaches to drawing background (absence) points, and (iii) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved using a global dataset for model training, rather than restricting data input to the species' native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e., into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g., boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post hoc test conducted on a new Parthenium dataset from Nepal validated excellent predictive performance of our 'best' model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for parthenium

  15. Secondary Metabolite Profiles and Mating Populations of Fusarium species in Section Liseola Associated with Bakanae Disease of Rice

    Directory of Open Access Journals (Sweden)

    Nur Ain Izzati, M. Z.

    2008-01-01

    Full Text Available A total of 25 strains of Fusarium species that belong to F. fujikuroi (a pathogen of bakanae disease, F. proliferatum, F. sacchari, F. subglutinans and F. verticillioides were isolated from rice plants showing typical bakanae symptoms in Malaysia and Indonesia and screened for their secondary metabolites. The objectives of the studies were to determine the physiological variability based on production of moniliformin (MON, fumonisin (FB1, gibberellic acid (GA3 and fusaric acid (FA as well as to ascertain the mating populations (MPs within the Gibberella fujikuroi species complex based on their ability to produce perithecia and viable ascospores. Production of GA3 could be used to separate F. fujikuroi that belongs to MP-C from other species. In crosses with seven standard testers of MPs, 76% of strains could be assigned to at least one of the G. fujikuroi species complex namely MP-A (G. moniliformis, MP-B (G. sacchari, MP-C (G. fujikuroi and MP-D (G. intermedia. Single strain (M3237P that was assigned as MP-C, and has also been identified morphologically as F. fujikuroi was also crossed-fertile with MP-D tester. The secondary metabolites profiles and the presence of MP-A, MP-B, MP-C and MP-D strains on samples of bakanae-infected rice plants are new records in Malaysia.

  16. BAYESIAN MODELS FOR SPECIES DISTRIBUTION MODELLING WITH ONLY-PRESENCE RECORDS

    Directory of Open Access Journals (Sweden)

    Bartolo de Jesús Villar-Hernández

    2015-08-01

    Full Text Available One of the central issues in ecology is the study of geographical distribution of species of flora and fauna through Species Distribution Models (SDM. Recently, scientific interest has focused on presence-only records. Two recent approaches have been proposed for this problem: a model based on maximum likelihood method (Maxlike and an inhomogeneous poisson process model (IPP. In this paper we discussed two bayesian approaches called MaxBayes and IPPBayes based on Maxlike and IPP model, respectively. To illustrate these proposals, we implemented two study examples: (1 both models were implemented on a simulated dataset, and (2 we modeled the potencial distribution of genus Dalea in the Tehuacan-Cuicatlán biosphere reserve with both models, the results was compared with that of Maxent. The results show that both models, MaxBayes and IPPBayes, are viable alternatives when species distribution are modeled with only-presence records. For simulated dataset, MaxBayes achieved prevalence estimation, even when the number of records was small. In the real dataset example, both models predict similar potential distributions like Maxent does. Â

  17. A mechanistic approach to link biological effects of radioactive substances from molecules to populations in wildlife species - A mechanistic approach to link biological effects of radionuclides from molecules to populations in wildlife species

    Energy Technology Data Exchange (ETDEWEB)

    Alonzo, Frederic; Parisot, Florian; Plaire, Delphine; Adam-Guillermin, Christelle; Garnier- Laplace, Jacqueline [Institut de Radioprotection et de Surete Nucleaire (IRSN), PRP-ENV, SERIS, LECO, Cadarache, Saint-Paul- Lez-Durance, 13115 (France)

    2014-07-01

    Understanding how toxic contaminants affect wildlife species at various levels of biological organisation (sub-cellular, histological, physiological, organism, population levels) is a major research goal in both ecotoxicology and radioecology. A mechanistic understanding of the links between the different observed perturbations is necessary to predict consequences for survival, growth and reproduction which are critical for population dynamics. However, time scales at which such links are established in the laboratory are rarely relevant for natural populations. With a small size and short life cycle, the cladoceran micro-crustacean Daphnia magna is a particularly suitable biological model for studying effects of radioactive contaminants over several generations. Multi-generational exposures are much more representative of the environmental context of field populations for which contaminations can last for durations which largely exceed individual longevity and involve exposure of many successive generations. Over the last decade, multi-generational investigations of toxic effects were conducted under controlled conditions in D. magna exposed to various radionuclides including depleted uranium, americium-241 and cesium-137, representing respectively a dominantly chemo-toxic metal, an alpha internal contamination and a gamma external radiation. Results showed in all cases that toxic effects on physiology and life history (survival, body size, fecundity) increased in severity across generations. These observations demonstrated that measured effects in one generation might not be representative of toxicity in the following offspring generations, and ultimately of the population response. Reduction in somatic growth and reproduction induced by uranium were analysed using the mechanistic modelling approach known as DEBtox (model of dynamic energy budget applied to toxicology). Modelling results suggested that uranium primarily affects assimilation. This metabolic mode

  18. Evaluating species richness: biased ecological inference results from spatial heterogeneity in species detection probabilities

    Science.gov (United States)

    McNew, Lance B.; Handel, Colleen M.

    2015-01-01

    Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multi-species occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real dataset of bird observations in northwestern Alaska, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results

  19. Local extinction and recolonization, species effective population size, and modern human origins.

    Science.gov (United States)

    Eller, Elise; Hawks, John; Relethford, John H

    2004-10-01

    A primary objection from a population genetics perspective to a multiregional model of modern human origins is that the model posits a large census size, whereas genetic data suggest a small effective population size. The relationship between census size and effective size is complex, but arguments based on an island model of migration show that if the effective population size reflects the number of breeding individuals and the effects of population subdivision, then an effective population size of 10,000 is inconsistent with the census size of 500,000 to 1,000,000 that has been suggested by archeological evidence. However, these models have ignored the effects of population extinction and recolonization, which increase the expected variance among demes and reduce the inbreeding effective population size. Using models developed for population extinction and recolonization, we show that a large census size consistent with the multiregional model can be reconciled with an effective population size of 10,000, but genetic variation among demes must be high, reflecting low interdeme migration rates and a colonization process that involves a small number of colonists or kin-structured colonization. Ethnographic and archeological evidence is insufficient to determine whether such demographic conditions existed among Pleistocene human populations, and further work needs to be done. More realistic models that incorporate isolation by distance and heterogeneity in extinction rates and effective deme sizes also need to be developed. However, if true, a process of population extinction and recolonization has interesting implications for human demographic history.

  20. Estimating Lion Abundance using N-mixture Models for Social Species.

    Science.gov (United States)

    Belant, Jerrold L; Bled, Florent; Wilton, Clay M; Fyumagwa, Robert; Mwampeta, Stanslaus B; Beyer, Dean E

    2016-10-27

    Declining populations of large carnivores worldwide, and the complexities of managing human-carnivore conflicts, require accurate population estimates of large carnivores to promote their long-term persistence through well-informed management We used N-mixture models to estimate lion (Panthera leo) abundance from call-in and track surveys in southeastern Serengeti National Park, Tanzania. Because of potential habituation to broadcasted calls and social behavior, we developed a hierarchical observation process within the N-mixture model conditioning lion detectability on their group response to call-ins and individual detection probabilities. We estimated 270 lions (95% credible interval = 170-551) using call-ins but were unable to estimate lion abundance from track data. We found a weak negative relationship between predicted track density and predicted lion abundance from the call-in surveys. Luminosity was negatively correlated with individual detection probability during call-in surveys. Lion abundance and track density were influenced by landcover, but direction of the corresponding effects were undetermined. N-mixture models allowed us to incorporate multiple parameters (e.g., landcover, luminosity, observer effect) influencing lion abundance and probability of detection directly into abundance estimates. We suggest that N-mixture models employing a hierarchical observation process can be used to estimate abundance of other social, herding, and grouping species.

  1. Geometric and morphometric analysis of fish scales to identity genera, species and populations case study: the Cyprinid family

    Directory of Open Access Journals (Sweden)

    Seyedeh Narjes Tabatabei

    2014-01-01

    Full Text Available Using fish scale to identity species and population is a rapid, safe and low cost method. Hence, this study was carried out to investigate the possibility of using geometric and morphometric methods in fish scales for rapid identification of species and populations and compare the efficiency of applying few and/or high number of landmark points. For this purpose, scales of one population of Luciobarbus capito, four populations of Alburnoides eichwaldii and two populations of Rutilus frisii kutum, all belonging to cyprinid family, were examined. On two-dimensional images of the scales 7 and 23 landmark points were digitized in two separate times using TpsDig2, respectively. Landmark data after generalized procrustes analysis were analyzed using Principal Component Analysis (PCA, Canonical Variate Analysis (CVA and Cluster Analysis. The results of both methods (using 7 and 23 landmark points showed significant differences of the shape of scales among the three species studied (P0.05. The results also showed that few number of landmarks could display the differences between scale shapes. According to the results of this study, it could be stated that the scale of each species had unique shape patterns which could be utilized as a species identification key.

  2. Reduction of structured population models to threshold-type delay equations and functional differential equations: A case study

    Energy Technology Data Exchange (ETDEWEB)

    Smith, H.L. (Arizona State Univ., Tempe (United States))

    1993-01-01

    It is shown by way of a simple example that certain structured population models lead naturally to differential delay equations of the threshold type and that these equations can be transformed in a natural way to functional differential equations. The model examined can be viewed as a model of competition between adults and juveniles of a single population. The results indicate the possibility that this competition leads to instability. 28 refs., 2 figs.

  3. Theoretical models of the impact of climate change on natural populations, communities and ecosystems. Final report, 1989--1992

    Energy Technology Data Exchange (ETDEWEB)

    Wiegert, R.

    1992-12-31

    Land use change is a relatively understudied aspect of global change. In many cases, the impact of land use on plant and animal species may be far greater than the impact of climate change per se. As an integral part of our long-term studies of the response of animal populations to global change, we have focused on land use change as a dominant driving force. Climate change, no doubt, will also play a role in determining the future abundance and distribution of many species, but, for many species, the signal from climate change per se may be difficult to detect if we do not first understand the impact of land use change. This formed the dominant theme of the research by the PI (Pulliam). Both land use change and year to year climate change can directly affect other populations and two examples of this formed the focus of the remaining research, models of invertebrates in Carolina Bays and a model of a commercial estuarine population of blue crabs.

  4. Recent Demographic History and Present Fine-Scale Structure in the Northwest Atlantic Leatherback (Dermochelys coriacea) Turtle Population

    Science.gov (United States)

    Molfetti, Érica; Torres Vilaça, Sibelle; Georges, Jean-Yves; Plot, Virginie; Delcroix, Eric; Le Scao, Rozen; Lavergne, Anne; Barrioz, Sébastien; dos Santos, Fabrício Rodrigues; de Thoisy, Benoît

    2013-01-01

    The leatherback turtle Dermochelys coriacea is the most widely distributed sea turtle species in the world. It exhibits complex life traits: female homing and migration, migrations of juveniles and males that remain poorly known, and a strong climatic influence on resources, breeding success and sex-ratio. It is consequently challenging to understand population dynamics. Leatherbacks are critically endangered, yet the group from the Northwest Atlantic is currently considered to be under lower risk than other populations while hosting some of the largest rookeries. Here, we investigated the genetic diversity and the demographic history of contrasted rookeries from this group, namely two large nesting populations in French Guiana, and a smaller one in the French West Indies. We used 10 microsatellite loci, of which four are newly isolated, and mitochondrial DNA sequences of the control region and cytochrome b. Both mitochondrial and nuclear markers revealed that the Northwest Atlantic stock of leatherbacks derives from a single ancestral origin, but show current genetic structuration at the scale of nesting sites, with the maintenance of migrants amongst rookeries. Low nuclear genetic diversities are related to founder effects that followed consequent bottlenecks during the late Pleistocene/Holocene. Most probably in response to climatic oscillations, with a possible influence of early human hunting, female effective population sizes collapsed from 2 million to 200. Evidence of founder effects and high numbers of migrants make it possible to reconsider the population dynamics of the species, formerly considered as a metapopulation model: we propose a more relaxed island model, which we expect to be a key element in the currently observed recovering of populations. Although these Northwest Atlantic rookeries should be considered as a single evolutionary unit, we stress that local conservation efforts remain necessary since each nesting site hosts part of the genetic

  5. FUNDAMENTAL ASPECTS OF EPISODIC ACCRETION CHEMISTRY EXPLORED WITH SINGLE-POINT MODELS

    International Nuclear Information System (INIS)

    Visser, Ruud; Bergin, Edwin A.

    2012-01-01

    We explore a set of single-point chemical models to study the fundamental chemical aspects of episodic accretion in low-mass embedded protostars. Our goal is twofold: (1) to understand how the repeated heating and cooling of the envelope affects the abundances of CO and related species; and (2) to identify chemical tracers that can be used as a novel probe of the timescales and other physical aspects of episodic accretion. We develop a set of single-point models that serve as a general prescription for how the chemical composition of a protostellar envelope is altered by episodic accretion. The main effect of each accretion burst is to drive CO ice off the grains in part of the envelope. The duration of the subsequent quiescent stage (before the next burst hits) is similar to or shorter than the freeze-out timescale of CO, allowing the chemical effects of a burst to linger long after the burst has ended. We predict that the resulting excess of gas-phase CO can be observed with single-dish or interferometer facilities as evidence of an accretion burst in the past 10 3 -10 4 yr.

  6. On population in a polluted patchy environment

    International Nuclear Information System (INIS)

    He, J; Wang, K

    2008-01-01

    In this paper, the effect of diffusion on the permanence of a species in a polluted patchy environment is studied. We set up a single species diffusive system on a region composed of two patches, one of which is contaminated and the other is clear. When there is no diffusion and the exogenous toxicant concentration exceeds some a value, the population in the polluted patch will go to extinction. When the diffusion exists, we give suitable conditions for the permanence or extinction of the population in the system

  7. [Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants].

    Science.gov (United States)

    Boronnikova, S V; Kalendar', R N

    2010-01-01

    Species-specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm' region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP-markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

  8. Integrated population modeling of black bears in Minnesota: implications for monitoring and management.

    Science.gov (United States)

    Fieberg, John R; Shertzer, Kyle W; Conn, Paul B; Noyce, Karen V; Garshelis, David L

    2010-08-12

    Wildlife populations are difficult to monitor directly because of costs and logistical challenges associated with collecting informative abundance data from live animals. By contrast, data on harvested individuals (e.g., age and sex) are often readily available. Increasingly, integrated population models are used for natural resource management because they synthesize various relevant data into a single analysis. We investigated the performance of integrated population models applied to black bears (Ursus americanus) in Minnesota, USA. Models were constructed using sex-specific age-at-harvest matrices (1980-2008), data on hunting effort and natural food supplies (which affects hunting success), and statewide mark-recapture estimates of abundance (1991, 1997, 2002). We compared this approach to Downing reconstruction, a commonly used population monitoring method that utilizes only age-at-harvest data. We first conducted a large-scale simulation study, in which our integrated models provided more accurate estimates of population trends than did Downing reconstruction. Estimates of trends were robust to various forms of model misspecification, including incorrectly specified cub and yearling survival parameters, age-related reporting biases in harvest data, and unmodeled temporal variability in survival and harvest rates. When applied to actual data on Minnesota black bears, the model predicted that harvest rates were negatively correlated with food availability and positively correlated with hunting effort, consistent with independent telemetry data. With no direct data on fertility, the model also correctly predicted 2-point cycles in cub production. Model-derived estimates of abundance for the most recent years provided a reasonable match to an empirical population estimate obtained after modeling efforts were completed. Integrated population modeling provided a reasonable framework for synthesizing age-at-harvest data, periodic large-scale abundance estimates, and

  9. Age, growth and population structure of invasive lionfish (Pterois volitans/miles in northeast Florida using a length-based, age-structured population model

    Directory of Open Access Journals (Sweden)

    Eric G. Johnson

    2016-12-01

    Full Text Available The effective management of invasive species requires detailed understanding of the invader’s life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish (Pterois volitans/miles have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1 lionfish exhibited rapid growth with seasonal variation in growth rates; (2 distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3 the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water.

  10. Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model.

    Science.gov (United States)

    Johnson, Eric G; Swenarton, Mary Katherine

    2016-01-01

    The effective management of invasive species requires detailed understanding of the invader's life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish ( Pterois volitans/miles ) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates; (2) distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3) the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water.

  11. Baselines to detect population stability of the threatened alpine plant Packera franciscana (Asteraceae)

    Science.gov (United States)

    James F. Fowler; Carolyn Hull Sieg; Shaula Hedwall

    2015-01-01

    Population size and density estimates have traditionally been acceptable ways to track species’ response to changing environments; however, species' population centroid elevation has recently been an equally important metric. Packera franciscana (Greene) W.A. Weber and A. Love (Asteraceae; San Francisco Peaks ragwort) is a single mountain endemic plant found only...

  12. Microsatellite Primers in the Foundation Tree Species Pinus edulis and P. monophylla (Pinaceae

    Directory of Open Access Journals (Sweden)

    Andrew L. Krohn

    2013-07-01

    Full Text Available Premise of the study: Microsatellite primers were developed in the foundational tree species Pinus edulis to investigate population differentiation of P. edulis and hybridization among closely related species. Methods and Results: Using a hybridization protocol, primer sets for 11 microsatellite loci were developed using megagametophyte tissue from P. edulis and scored for polymorphism in three populations of P. edulis and a single P. monophylla population. The primers amplified simple and compound di-, tri-, and pentanucleotide repeats with two to 18 alleles per locus. Conclusions: These results demonstrate the utility of the described primers for studies of population differentiation within and among P. edulis populations as well as across putative hybrid zones where P. edulis may coexist with sister species.

  13. The Accuracy and Bias of Single-Step Genomic Prediction for Populations Under Selection

    Directory of Open Access Journals (Sweden)

    Wan-Ling Hsu

    2017-08-01

    Full Text Available In single-step analyses, missing genotypes are explicitly or implicitly imputed, and this requires centering the observed genotypes using the means of the unselected founders. If genotypes are only available for selected individuals, centering on the unselected founder mean is not straightforward. Here, computer simulation is used to study an alternative analysis that does not require centering genotypes but fits the mean μg of unselected individuals as a fixed effect. Starting with observed diplotypes from 721 cattle, a five-generation population was simulated with sire selection to produce 40,000 individuals with phenotypes, of which the 1000 sires had genotypes. The next generation of 8000 genotyped individuals was used for validation. Evaluations were undertaken with (J or without (N μg when marker covariates were not centered; and with (JC or without (C μg when all observed and imputed marker covariates were centered. Centering did not influence accuracy of genomic prediction, but fitting μg did. Accuracies were improved when the panel comprised only quantitative trait loci (QTL; models JC and J had accuracies of 99.4%, whereas models C and N had accuracies of 90.2%. When only markers were in the panel, the 4 models had accuracies of 80.4%. In panels that included QTL, fitting μg in the model improved accuracy, but had little impact when the panel contained only markers. In populations undergoing selection, fitting μg in the model is recommended to avoid bias and reduction in prediction accuracy due to selection.

  14. Inverse modeling of multicomponent reactive transport through single and dual porosity media

    Science.gov (United States)

    Samper, Javier; Zheng, Liange; Fernández, Ana María; Montenegro, Luis

    2008-06-01

    Compacted bentonite is foreseen as buffer material for high-level radioactive waste in deep geological repositories because it provides hydraulic isolation, chemical stability, and radionuclide sorption. A wide range of laboratory tests were performed within the framework of FEBEX ( Full-scale Engineered Barrier EXperiment) project to characterize buffer properties and develop numerical models for FEBEX bentonite. Here we present inverse single and dual-continuum multicomponent reactive transport models of a long-term permeation test performed on a 2.5 cm long sample of FEBEX bentonite. Initial saline bentonite porewater was flushed with 5.5 pore volumes of fresh granitic water. Water flux and chemical composition of effluent waters were monitored during almost 4 years. The model accounts for solute advection and diffusion and geochemical reactions such as aqueous complexation, acid-base, cation exchange, protonation/deprotonation by surface complexation and dissolution/precipitation of calcite, chalcedony and gypsum. All of these processes are assumed at local equilibrium. Similar to previous studies of bentonite porewater chemistry on batch systems which attest the relevance of protonation/deprotonation on buffering pH, our results confirm that protonation/deprotonation is a key process in maintaining a stable pH under dynamic transport conditions. Breakthrough curves of reactive species are more sensitive to initial porewater concentration than to effective diffusion coefficient. Optimum estimates of initial porewater chemistry of saturated compacted FEBEX bentonite are obtained by solving the inverse problem of multicomponent reactive transport. While the single-continuum model reproduces the trends of measured data for most chemical species, it fails to match properly the long tails of most breakthrough curves. Such limitation is overcome by resorting to a dual-continuum reactive transport model.

  15. Genetic diversity of Kenyan Prosopis populations based on random amplified polymorphic DNA markers

    NARCIS (Netherlands)

    Muturi, G.M.; Machua, J.M.; Mohren, G.M.J.; Poorter, L.; Gicheru, J.M.; Maina, L.W.

    2012-01-01

    Several Prosopis species and provenances were introduced in Kenya, either as a single event or repeatedly. To date, naturally established Prosopis populations are described as pure species depending on site, despite the aforementioned introduction of several species within some sites. To determine

  16. Reproductive characteristics and population decline of four species of skate (Rajidae) off the eastern coast of Canada.

    Science.gov (United States)

    Mcphie, R P; Campana, S E

    2009-07-01

    Four of the most common species of skate (Rajidae) were studied off eastern Canada to determine if their reproductive characteristics were linked to their population trajectories. The fecundity of the winter skate Leucoraja ocellata, the little skate Leucoraja erinacea, the thorny skate Amblyraja radiata and the smooth skate Malacoraja senta averaged between 41 and 56 egg cases per year for each species. For all species but L. ocellata, males matured at larger sizes and at later ages than females. Theoretical rates of population increase for non-equilibrium populations of L. ocellata (c. 0.07), M. senta (c. 0.14) and L. erinacea and A. radiata (c. 0.20) were low compared to most fishes, indicating that north-west Atlantic skates are intrinsically unproductive, yet are theoretically capable of supporting low-level fisheries. Nevertheless, the results of 36 years of research surveys indicate that the abundance of mature L. ocellata, A. radiata and M. senta all decreased by >90% since 1970, indicating that past fishing mortality (both directed and undirected) has outstripped the net productivity of the skate populations on the eastern Scotian Shelf. The relationship between maximum age (t(max)) and age of maturity (t(mat)) was a better predictor of population growth rate than was body size, with the species exhibiting the highest ratios of t(mat) :t(max) (L. ocellata = 0.68, M. senta = 0.66) having the lowest predicted population growth rates. L. ocellata appears to have the lowest productivity and has experienced the greatest population decline, thus raising concerns over its future status.

  17. Gene flow among established Puerto Rican populations of the exotic tree species, Albizia lebbeck.

    Science.gov (United States)

    Dunphy, B K; Hamrick, J L

    2005-04-01

    We estimate gene flow and patterns of genetic diversity in Albizia lebbeck, an invasive leguminous tree in the dry forest of southwestern Puerto Rico. Genetic diversity estimates calculated for 10 populations of 24 trees each indicated that these populations may have been formed from multiple introductions. The presence of unique genotypes in the northernmost populations suggests that novel genotypes are still immigrating into the area. This combination of individuals from disparate locations led to high estimates of genetic diversity (He = 0.266, P = 0.67). Indirect estimates of gene flow indicate that only 0.69 migrants per generation move between populations, suggesting that genetic diversity within populations should decrease due to genetic drift. Since migration-drift equilibrium was not found, however, this estimate needs to be viewed with caution. The regular production of pods in this outcrossing species (tm = 0.979) indicates that sufficient outcross pollen is received to insure successful reproduction. Direct estimates of gene flow indicate that between 44 and 100% of pollen received by trees in four small stands of trees (n < 11) was foreign. The role of gene flow in facilitating the spread of this invasive plant species is discussed.

  18. Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

    KAUST Repository

    Horne, J. B.

    2013-01-11

    Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged. © 2013 The Authors. Journal

  19. Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

    KAUST Repository

    Horne, J. B.; van Herwerden, L.

    2013-01-01

    Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged. © 2013 The Authors. Journal

  20. Terrestrial population models for ecological risk assessment: A state-of-the-art review

    Science.gov (United States)

    Emlen, J.M.

    1989-01-01

    Few attempts have been made to formulate models for predicting impacts of xenobiotic chemicals on wildlife populations. However, considerable effort has been invested in wildlife optimal exploitation models. Because death from intoxication has a similar effect on population dynamics as death by harvesting, these management models are applicable to ecological risk assessment. An underlying Leslie-matrix bookkeeping formulation is widely applicable to vertebrate wildlife populations. Unfortunately, however, the various submodels that track birth, death, and dispersal rates as functions of the physical, chemical, and biotic environment are by their nature almost inevitably highly species- and locale-specific. Short-term prediction of one-time chemical applications requires only information on mortality before and after contamination. In such cases a simple matrix formulation may be adequate for risk assessment. But generally, risk must be projected over periods of a generation or more. This precludes generic protocols for risk assessment and also the ready and inexpensive predictions of a chemical's influence on a given population. When designing and applying models for ecological risk assessment at the population level, the endpoints (output) of concern must be carefully and rigorously defined. The most easily accessible and appropriate endpoints are (1) pseudoextinction (the frequency or probability of a population falling below a prespecified density), and (2) temporal mean population density. Spatial and temporal extent of predicted changes must be clearly specified a priori to avoid apparent contradictions and confusion.

  1. The accuracy of matrix population model projections for coniferous trees in the Sierra Nevada, California

    Science.gov (United States)

    van Mantgem, P.J.; Stephenson, N.L.

    2005-01-01

    1 We assess the use of simple, size-based matrix population models for projecting population trends for six coniferous tree species in the Sierra Nevada, California. We used demographic data from 16 673 trees in 15 permanent plots to create 17 separate time-invariant, density-independent population projection models, and determined differences between trends projected from initial surveys with a 5-year interval and observed data during two subsequent 5-year time steps. 2 We detected departures from the assumptions of the matrix modelling approach in terms of strong growth autocorrelations. We also found evidence of observation errors for measurements of tree growth and, to a more limited degree, recruitment. Loglinear analysis provided evidence of significant temporal variation in demographic rates for only two of the 17 populations. 3 Total population sizes were strongly predicted by model projections, although population dynamics were dominated by carryover from the previous 5-year time step (i.e. there were few cases of recruitment or death). Fractional changes to overall population sizes were less well predicted. Compared with a null model and a simple demographic model lacking size structure, matrix model projections were better able to predict total population sizes, although the differences were not statistically significant. Matrix model projections were also able to predict short-term rates of survival, growth and recruitment. Mortality frequencies were not well predicted. 4 Our results suggest that simple size-structured models can accurately project future short-term changes for some tree populations. However, not all populations were well predicted and these simple models would probably become more inaccurate over longer projection intervals. The predictive ability of these models would also be limited by disturbance or other events that destabilize demographic rates. ?? 2005 British Ecological Society.

  2. The aggregate site frequency spectrum for comparative population genomic inference.

    Science.gov (United States)

    Xue, Alexander T; Hickerson, Michael J

    2015-12-01

    Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent postglacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multilevel statistical frameworks to test models involving assemblages and/or communities, and as large-scale SNP data from nonmodel species become routine, the aSFS expands the potential for powerful next-generation comparative population genomic inference. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  3. Modeling the fish community population dynamics and forecasting the eradication success of an exotic fish from an alpine stream

    Science.gov (United States)

    Laplanche, Christophe; Elger, Arnaud; Santoul, Frédéric; Thiede, Gary P.; Budy, Phaedra

    2018-01-01

    Management actions aimed at eradicating exotic fish species from riverine ecosystems can be better informed by forecasting abilities of mechanistic models. We illustrate this point with an example of the Logan River, Utah, originally populated with endemic cutthroat trout (Oncorhynchus clarkii utah), which compete with exotic brown trout (Salmo trutta). The coexistence equilibrium was disrupted by a large scale, experimental removal of the exotic species in 2009–2011 (on average, 8.2% of the stock each year), followed by an increase in the density of the native species. We built a spatially-explicit, reaction-diffusion model encompassing four key processes: population growth in heterogeneous habitat, competition, dispersal, and a management action. We calibrated the model with detailed long-term monitoring data (2001–2016) collected along the 35.4-km long river main channel. Our model, although simple, did a remarkable job reproducing the system steady state prior to the management action. Insights gained from the model independent predictions are consistent with available knowledge and indicate that the exotic species is more competitive; however, the native species still occupies more favorable habitat upstream. Dynamic runs of the model also recreated the observed increase of the native species following the management action. The model can simulate two possible distinct long-term outcomes: recovery or eradication of the exotic species. The processing of available knowledge using Bayesian methods allowed us to conclude that the chance for eradication of the invader was low at the beginning of the experimental removal (0.7% in 2009) and increased (20.5% in 2016) by using more recent monitoring data. We show that accessible mathematical and numerical tools can provide highly informative insights for managers (e.g., outcome of their conservation actions), identify knowledge gaps, and provide testable theory for researchers.

  4. Demographic models and IPCC climate projections predict the decline of an emperor penguin population

    Science.gov (United States)

    Jenouvrier, Stéphanie; Caswell, Hal; Barbraud, Christophe; Holland, Marika; Strœve, Julienne; Weimerskirch, Henri

    2009-01-01

    Studies have reported important effects of recent climate change on Antarctic species, but there has been to our knowledge no attempt to explicitly link those results to forecasted population responses to climate change. Antarctic sea ice extent (SIE) is projected to shrink as concentrations of atmospheric greenhouse gases (GHGs) increase, and emperor penguins (Aptenodytes forsteri) are extremely sensitive to these changes because they use sea ice as a breeding, foraging and molting habitat. We project emperor penguin population responses to future sea ice changes, using a stochastic population model that combines a unique long-term demographic dataset (1962–2005) from a colony in Terre Adélie, Antarctica and projections of SIE from General Circulation Models (GCM) of Earth's climate included in the most recent Intergovernmental Panel on Climate Change (IPCC) assessment report. We show that the increased frequency of warm events associated with projected decreases in SIE will reduce the population viability. The probability of quasi-extinction (a decline of 95% or more) is at least 36% by 2100. The median population size is projected to decline from ≈6,000 to ≈400 breeding pairs over this period. To avoid extinction, emperor penguins will have to adapt, migrate or change the timing of their growth stages. However, given the future projected increases in GHGs and its effect on Antarctic climate, evolution or migration seem unlikely for such long lived species at the remote southern end of the Earth. PMID:19171908

  5. Clutch size in populations and species of cnemidophorines (Squamata: Teiidae on the eastern coast of Brazil

    Directory of Open Access Journals (Sweden)

    VANDERLAINE A. MENEZES

    2014-06-01

    Full Text Available We analyzed some reproductive aspects of 16 coastal populations, belonging to five lizard species (A. ocellifera, A. abaetensis, A. nativo, A. littoralis and C. lacertoides from different restinga habitats along the eastern coast of Brazil. This study aimed to evaluate to what extent the reproductive aspects vary geographically and among species. For each female, we recorded the number of vitellogenic follicles, size and color of the largest follicle, presence and size of corpora lutea, and number and size of oviductal eggs. Clutch size of almost all coastal populations/species of Ameivula had little variation and most clutches were composed of two eggs. There was a significant relationship between female size and the mean clutch size when females from different species were pooled. Mean egg volume, among species, varied from 420 to 655 mm3. Relative clutch mass varied from 0.129 to 0.159 and did not differ significantly among species. We concluded that the five coastal species studied (four bisexuals and one parthenogenetic had similar reproductive characteristics. Most of them presented multiple clutches, low clutch size and low relative clutch mass, similar to other species in the genus and to unisexual and bisexual species of the Teiidae family.

  6. A Study of Naturally Acquired Canine Babesiosis Caused by Single and Mixed Babesia Species in Zambia: Clinicopathological Findings and Case Management

    Directory of Open Access Journals (Sweden)

    King Shimumbo Nalubamba

    2015-01-01

    Full Text Available A retrospective and prospective analysis of clinical records of dogs diagnosed with Babesia infections was carried out for the years 2000 to 2013 from practices in Lusaka, Zambia. Records of 363 dogs with confirmed Babesia infections were analysed using demographic factors including sex, breed, age, and clinical signs in relation to haematological findings and Babesia species. The clinical and laboratory findings observed are described as well as Babesia species identification. The study included 18 breeds and the highest proportion were mongrels (32.2%, males representing 64.5% of the population. The most common presenting problems were anorexia (65.3% and lethargy/weakness (65.3%. The most common clinical signs were fever (87.3%, pallor (52.3%, lymphadenopathy (47.4%, and presence of ticks (44.9%. Anaemia (96.4% and nucleated erythrocytes (42.2% were the most common laboratory findings. A mixed infection of Babesia rossi and Babesia gibsoni was present in 59.7% of dogs, whilst 8% and 32.2% had B. rossi and B. gibsoni as a single infection, respectively. Case management mainly involved therapy with tetracyclines and imidocarb and was usually accompanied by clinical improvement. This study highlights, for the first time, the presence of B. gibsoni in natural dog populations in Zambia, where previously only B. rossi was reported.

  7. Malthusian Catastrophe: Species Extinction Caused By Oversized Population

    OpenAIRE

    Pan, Xubin

    2017-01-01

    There is one pseudo-extinction debt and four occurring conditions for real extinction debt. Since small and oversized populations have a high extinction risk, Pan threshold (upper limit) was calculated for Verhulst-Pear logistic growth model and logistic model with the Allee effect, an important parameter corresponding to Allee threshold (lower limit).

  8. Lattice Three-Species Models of the Spatial Spread of Rabies among FOXES

    Science.gov (United States)

    Benyoussef, A.; Boccara, N.; Chakib, H.; Ez-Zahraouy, H.

    Lattice models describing the spatial spread of rabies among foxes are studied. In these models, the fox population is divided into three-species: susceptible (S), infected or incubating (I), and infectious or rabid (R). They are based on the fact that susceptible and incubating foxes are territorial while rabid foxes have lost their sense of direction and move erratically. Two different models are investigated: a one-dimensional coupled-map lattice model, and a two-dimensional automata network model. Both models take into account the short-range character of the infection process and the diffusive motion of rabid foxes. Numerical simulations show how the spatial distribution of rabies, and the speed of propagation of the epizootic front depend upon the carrying capacity of the environment and diffusion of rabid foxes out of their territory.

  9. Comparison of stellar population model predictions using optical and infrared spectroscopy

    Science.gov (United States)

    Baldwin, C.; McDermid, R. M.; Kuntschner, H.; Maraston, C.; Conroy, C.

    2018-02-01

    We present Gemini/GNIRS cross-dispersed near-infrared spectra of 12 nearby early-type galaxies, with the aim of testing commonly used stellar population synthesis models. We select a subset of galaxies from the ATLAS3D sample which span a wide range of ages (single stellar population equivalent ages of 1-15 Gyr) at approximately solar metallicity. We derive star formation histories using four different stellar population synthesis models, namely those of Bruzual & Charlot, Conroy, Gunn & White, Maraston & Strömbäck and Vazdekis et al. We compare star formation histories derived from near-infrared spectra with those derived from optical spectra using the same models. We find that while all models agree in the optical, the derived star formation histories vary dramatically from model to model in the near-infrared. We find that this variation is largely driven by the choice of stellar spectral library, such that models including high-quality spectral libraries provide the best fits to the data, and are the most self-consistent when comparing optically derived properties with near-infrared ones. We also find the impact of age variation in the near-infrared to be subtle, and largely encoded in the shape of the continuum, meaning that the common approach of removing continuum information with a high-order polynomial greatly reduces our ability to constrain ages in the near-infrared.

  10. Development of a practical modeling framework for estimating the impact of wind technology on bird populations

    Energy Technology Data Exchange (ETDEWEB)

    Morrison, M.L. [California State Univ., Sacramento, CA (United States); Pollock, K.H. [North Carolina State Univ., Raleigh, NC (United States)

    1997-11-01

    One of the most pressing environmental concerns related to wind project development is the potential for avian fatalities caused by the turbines. The goal of this project is to develop a useful, practical modeling framework for evaluating potential wind power plant impacts that can be generalized to most bird species. This modeling framework could be used to get a preliminary understanding of the likelihood of significant impacts to birds, in a cost-effective way. The authors accomplish this by (1) reviewing the major factors that can influence the persistence of a wild population; (2) briefly reviewing various models that can aid in estimating population status and trend, including methods of evaluating model structure and performance; (3) reviewing survivorship and population projections; and (4) developing a framework for using models to evaluate the potential impacts of wind development on birds.

  11. Development of a practical modeling framework for estimating the impact of wind technology on bird populations

    International Nuclear Information System (INIS)

    Morrison, M.L.; Pollock, K.H.

    1997-11-01

    One of the most pressing environmental concerns related to wind project development is the potential for avian fatalities caused by the turbines. The goal of this project is to develop a useful, practical modeling framework for evaluating potential wind power plant impacts that can be generalized to most bird species. This modeling framework could be used to get a preliminary understanding of the likelihood of significant impacts to birds, in a cost-effective way. The authors accomplish this by (1) reviewing the major factors that can influence the persistence of a wild population; (2) briefly reviewing various models that can aid in estimating population status and trend, including methods of evaluating model structure and performance; (3) reviewing survivorship and population projections; and (4) developing a framework for using models to evaluate the potential impacts of wind development on birds

  12. Threatened species richness along a Himalayan elevational gradient: quantifying the influences of human population density, range size, and geometric constraints.

    Science.gov (United States)

    Paudel, Prakash Kumar; Sipos, Jan; Brodie, Jedediah F

    2018-02-07

    A crucial step in conserving biodiversity is to identify the distributions of threatened species and the factors associated with species threat status. In the biodiversity hotspot of the Himalaya, very little is known about which locations harbour the highest diversity of threatened species and whether diversity of such species is related to area, mid-domain effects (MDE), range size, or human density. In this study, we assessed the drivers of variation in richness of threatened birds, mammals, reptiles, actinopterygii, and amphibians along an elevational gradient in Nepal Himalaya. Although geometric constraints (MDE), species range size, and human population density were significantly related to threatened species richness, the interaction between range size and human population density was of greater importance. Threatened species richness was positively associated with human population density and negatively associated with range size. In areas with high richness of threatened species, species ranges tend to be small. The preponderance of species at risk of extinction at low elevations in the subtropical biodiversity hotspot could be due to the double impact of smaller range sizes and higher human density.

  13. Mitochondrial DNA in wildlife forensic science: Species identification of tissues

    Science.gov (United States)

    Cronin, Matthew A.; Palmisciano, Daniel A.; Vyse, Ernest R.; Cameron, David G.

    1991-01-01

    A common problem in wildlife law enforcement is identifying the species of origin of carcasses, meat, or blood when morphological characters such as hair or bones are not available. Immunological and protein electrophoretic (allozyme or general protein) procedures have been used in species identification with considerable success (Bunch et al. 1976, McClymont et al. 1982, Wolfe 1983, Mardini 1984, Pex and Wolfe 1985, Dratch 1986), However, immunological tests often are not sensitive enough to distinguish closely related species. Furthermore, electrophoretically detectable protein polymorphisms may be lacking in certain populations or species and may not be species-specific.Analysis of DNA in human and wildlife forensics has been shown to be a potentially powerful tool for identification of individuals (Jeffreys et al. 1985, Vassartet al. 1987, Thommasen et al. 1989). Differences in copy number and nucleotide sequence of repetitive sequences in the nuclear (chromosomal) DNA result in hypervariability and individual-specific patterns which have been termed DNA "fingerprints." However, these patterns may be too variable for species identification necessitating analyses of more conservative parts of the genome.Mitochondrial DNA (mtDNA) is haploid, maternally inherited, similar in nucleotide sequence among conspecifics from the same geographic region, and more suitable for species identification, in contrast to hypervariable DNA fingerprints. MtDNA has several characteristics which make it useful as a species-specific marker. In mammals, individuals have a single mtDNA genotype shared by all tissues. Because mtDNA is haploid and reflects only maternal ancestry, the mtDNA gene number in a population is 4 times less than the nuclear gene number (Birky et al. 1983). This can result in relatively rapid loss or fixation of mtDNA genotypes so that all individuals in a population may be descended from a single ancestral female in as few as 4N (N = population size) generations

  14. Capillary Electrophoresis Single-Strand Conformational Polymorphisms as a Method to Differentiate Algal Species

    Directory of Open Access Journals (Sweden)

    Alice Jernigan

    2015-01-01

    Full Text Available Capillary electrophoresis single-strand conformational polymorphism (CE-SSCP was explored as a fast and inexpensive method to differentiate both prokaryotic (blue-green and eukaryotic (green and brown algae. A selection of two blue-green algae (Nostoc muscorum and Anabaena inaequalis, five green algae (Chlorella vulgaris, Oedogonium foveolatum, Mougeotia sp., Scenedesmus quadricauda, and Ulothrix fimbriata, and one brown algae (Ectocarpus sp. were examined and CE-SSCP electropherogram “fingerprints” were compared to each other for two variable regions of either the 16S or 18S rDNA gene. The electropherogram patterns were remarkably stable and consistent for each particular species. The patterns were unique to each species, although some common features were observed between the different types of algae. CE-SSCP could be a useful method for monitoring changes in an algae species over time as potential shifts in species occurred.

  15. A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations

    Science.gov (United States)

    Bonde, Robert K.; McGuire, Peter M.; Hunter, Margaret E.

    2012-01-01

    Managers faced with decisions on threatened and endangered wildlife populations often are lacking detailed information about the species of concern. Integration of genetic applications will provide management teams with a better ability to assess and monitor recovery efforts on imperiled species. The field of molecular biology continues to progress rapidly and many tools are currently available. Presently, little guidance is available to assist researchers and managers with the appropriate selection of genetic tools to study the status of wild manatee populations. We discuss several genetic tools currently employed in the application of conservation genetics, and address the utility of using these tools to determine population status to aid in conservation efforts. As an example, special emphasis is focused on the endangered West Indian manatee (Order Sirenia). All four extant species of sirenians are imperiled throughout their range, predominately due to anthropogenic sources; therefore, the need for genetic information on their population status is direly needed.

  16. Rapid and sensitive multiplex single-tube nested PCR for the identification of five human Plasmodium species.

    Science.gov (United States)

    Saito, Takahiro; Kikuchi, Aoi; Kaneko, Akira; Isozumi, Rie; Teramoto, Isao; Kimura, Masatsugu; Hirasawa, Noriyasu; Hiratsuka, Masahiro

    2018-06-01

    Malaria is caused by five species of Plasmodium in humans. Microscopy is currently used for pathogen detection, requiring considerable training and technical expertise as the parasites are often difficult to differentiate morphologically. Rapid diagnostic tests are as reliable as microscopy and offer faster diagnoses but possess lower detection limits and are incapable of distinguishing among the parasitic species. To improve global health efforts towards malaria control, a rapid, sensitive, species-specific, and economically viable diagnostic method is needed. In this study, we designed a malaria diagnostic method involving a multiplex single-tube nested PCR targeting Plasmodium mitochondrial cytochrome c oxidase III and single-stranded tag hybridization chromatographic printed-array strip. The detection sensitivity was found to be at least 40 times higher than that of agarose gel electrophoresis with ethidium bromide. This system also enables the identification of both single- and mixed-species malaria infections. The assay was validated with 152 Kenyan samples; using nested PCR as the standard, the assay's sensitivity and specificity were 88.7% and 100.0%, respectively. The turnaround time required, from PCR preparation to signal detection, is 90min. Our method should improve the diagnostic speed, treatment efficacy, and control of malaria, in addition to facilitating surveillance within global malaria eradication programs. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Multiscale Modeling of Microbial Communities

    Science.gov (United States)

    Blanchard, Andrew

    Although bacteria are single-celled organisms, they exist in nature primarily in the form of complex communities, participating in a vast array of social interactions through regulatory gene networks. The social interactions between individual cells drive the emergence of community structures, resulting in an intricate relationship across multiple spatiotemporal scales. Here, I present my work towards developing and applying the tools necessary to model the complex dynamics of bacterial communities. In Chapter 2, I utilize a reaction-diffusion model to determine the population dynamics for a population with two species. One species (CDI+) utilizes contact dependent inhibition to kill the other sensitive species (CDI-). The competition can produce diverse patterns, including extinction, coexistence, and localized aggregation. The emergence, relative abundance, and characteristic features of these patterns are collectively determined by the competitive benefit of CDI and its growth disadvantage for a given rate of population diffusion. The results provide a systematic and statistical view of CDI-based bacterial population competition, expanding the spectrum of our knowledge about CDI systems and possibly facilitating new experimental tests for a deeper understanding of bacterial interactions. In the following chapter, I present a systematic computational survey on the relationship between social interaction types and population structures for two-species communities by developing and utilizing a hybrid computational framework that combines discrete element techniques with reaction-diffusion equations. The impact of deleterious and beneficial interactions on the community are quantified. Deleterious interactions generate an increased variance in relative abundance, a drastic decrease in surviving lineages, and a rough expanding front. In contrast, beneficial interactions contribute to a reduced variance in relative abundance, an enhancement in lineage number, and a

  18. Population matrix models and palm resource management

    Directory of Open Access Journals (Sweden)

    1992-01-01

    Full Text Available MATRICES DE POPULATIONS ET MISE EN VALEUR DES PALMIERS. Au cours des 20 dernières années, les structures de population de nombreuses espèces de palmiers ont été décrites et discutées. La croissance et la stabilité des populations ont été analysées à l’aide de matrices. Dans cet article, nous reprenons un modèle et en discutons les aspects méthodologiques en vue d’une estimation des paramètres de l’histoire de la vie des palmiers. Les généralisations résultant de précédentes études sont présentées et les conséquences pour la mise en valeur des palmiers, concernant en particulier la confection de toitures, les fruits, la récolte des stipes, sont discutées. MATRICES DE POBLACIONES Y MANEJO DE PALMERAS. En los últimos 20 años, las estructuras de población de numerosas especies de palmeras han sido descritas y discutidas. El crecimiento y la estabilidad de las poblaciones han sido analizadas, utilizando matrices. En el presente artículo, presentamos un modelo y discutimos los aspectos metodológicos específicos para hacer una estimación de los parámetros de la historia de la vida de las palmeras. Son presentadas las generalizaciones diseñadas por estudios previos, y discutidas las implicancias en el manejo de las palmeras, en cuanto a techado, frutas, cosecha de los estípites. Population structures of numerous palm species have been described and discussed in the last 20 years. Population growth and stability have been analyzed with matrix models. In this paper we review matrix models and discuss methodological issues specific to estimating palm life history parameters. Generalizations drawn from previous studies are presented and implications for palm resource management, specifically for thatch, fruit, and stem harvest, are discussed.

  19. Nyala and Bushbuck I: A Competing Species Model.

    Science.gov (United States)

    Fay, Temple H.; Greeff, Johanna C.

    1999-01-01

    Introduces a model of differential equations for students--a very real overpopulation problem is occurring in the Ndumu Game Reserve in KwaZulu-Natal, South Africa, where one species of antelope, the Nyala, is crowding out another species, the Bushbuck. Constructs a competing species model to mathematically describe what is occurring in Ndumu.…

  20. 76 FR 15932 - Endangered and Threatened Species; Proposed Listing of Nine Distinct Population Segments of...

    Science.gov (United States)

    2011-03-22

    ... Loggerhead Sea Turtles as Endangered or Threatened AGENCIES: National Marine Fisheries Service (NMFS... Distinct Population Segments (DPS) of loggerhead sea turtles, Caretta caretta, as endangered or threatened... populations of loggerhead sea turtle'' as an endangered species under the ESA. NMFS published a notice in the...

  1. Global Population Structure of a Worldwide Pest and Virus Vector: Genetic Diversity and Population History of the Bemisia tabaci Sibling Species Group

    Science.gov (United States)

    2016-01-01

    The whitefly Bemisia tabaci sibling species (sibsp.) group comprises morphologically indiscernible lineages of well-known exemplars referred to as biotypes. It is distributed throughout tropical and subtropical latitudes and includes the contemporary invasive haplotypes, termed B and Q. Several well-studied B. tabaci biotypes exhibit ecological and biological diversity, however, most members are poorly studied or completely uncharacterized. Genetic studies have revealed substantial diversity within the group based on a fragment of the mitochondrial cytochrome oxidase I (mtCOI) sequence (haplotypes), with other tested markers being less useful for deep phylogenetic comparisons. The view of global relationships within the B. tabaci sibsp. group is largely derived from this single marker, making assessment of gene flow and genetic structure difficult at the population level. Here, the population structure was explored for B. tabaci in a global context using nuclear data from variable microsatellite markers. Worldwide collections were examined representing most of the available diversity, including known monophagous, polyphagous, invasive, and indigenous haplotypes. Well-characterized biotypes and other related geographic lineages discovered represented highly differentiated genetic clusters with little or no evidence of gene flow. The invasive B and Q biotypes exhibited moderate to high levels of genetic diversity, suggesting that they stemmed from large founding populations that have maintained ancestral variation, despite homogenizing effects, possibly due to human-mediated among-population gene flow. Results of the microsatellite analyses are in general agreement with published mtCOI phylogenies; however, notable conflicts exist between the nuclear and mitochondrial relationships, highlighting the need for a multifaceted approach to delineate the evolutionary history of the group. This study supports the hypothesis that the extant B. tabaci sibsp. group contains

  2. Disparity in population differentiation of sex-linked and autosomal variation in sibling species of the Jaera albifrons (Isopoda) complex

    DEFF Research Database (Denmark)

    Siegismund, H R

    2003-01-01

    The genetic variation at four enzyme loci is described for 22 populations of three Jaera species--J. albifrons, J. ischiosetosa, and J. praehirsuta--in the J. albifrons complex (Crustacea, Isopoda) in Denmark. The variation at three of the loci is similar, with the allele frequency spectra close...... to each other in all three species. An evolutionary tree based on the variation at these three loci revealed that the populations from the different species are completely intermixed in the tree. This was supported by hierarchical F-statistics where the between-species component was zero. At a fourth....... An evolutionary tree for this locus partitions the populations into separate groups and a hierarchical F-statistic has a between-species component of about 50%. The results are attributed to introgression with a higher rate for autosomes than for sex chromosomes....

  3. Modeling of Alkane Oxidation Using Constituents and Species

    Science.gov (United States)

    Bellan, Jasette; Harstad, Kenneth G.

    2010-01-01

    It is currently not possible to perform simulations of turbulent reactive flows due in particular to complex chemistry, which may contain thousands of reactions and hundreds of species. This complex chemistry results in additional differential equations, making the numerical solution of the equation set computationally prohibitive. Reducing the chemical kinetics mathematical description is one of several important goals in turbulent reactive flow modeling. A chemical kinetics reduction model is proposed for alkane oxidation in air that is based on a parallel methodology to that used in turbulence modeling in the context of the Large Eddy Simulation. The objective of kinetic modeling is to predict the heat release and temperature evolution. This kinetic mechanism is valid over a pressure range from atmospheric to 60 bar, temperatures from 600 K to 2,500 K, and equivalence ratios from 0.125 to 8. This range encompasses diesel, HCCI, and gas-turbine engines, including cold ignition. A computationally efficient kinetic reduction has been proposed for alkanes that has been illustrated for n-heptane using the LLNL heptane mechanism. This model is consistent with turbulence modeling in that scales were first categorized into either those modeled or those computed as progress variables. Species were identified as being either light or heavy. The heavy species were decomposed into defined 13 constituents, and their total molar density was shown to evolve in a quasi-steady manner. The light species behave either in a quasi-steady or unsteady manner. The modeled scales are the total constituent molar density, Nc, and the molar density of the quasi-steady light species. The progress variables are the total constituent molar density rate evolution and the molar densities of the unsteady light species. The unsteady equations for the light species contain contributions of the type gain/loss rates from the heavy species that are modeled consistent with the developed mathematical

  4. Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities.

    Science.gov (United States)

    Scholz, Christian F P; Jensen, Anders

    2017-01-01

    The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.

  5. Quantifying the effect of water activity and storage temperature on single spore lag times of three moulds isolated from spoiled bakery products.

    Science.gov (United States)

    Dagnas, Stéphane; Gougouli, Maria; Onno, Bernard; Koutsoumanis, Konstantinos P; Membré, Jeanne-Marie

    2017-01-02

    The inhibitory effect of water activity (a w ) and storage temperature on single spore lag times of Aspergillus niger, Eurotium repens (Aspergillus pseudoglaucus) and Penicillium corylophilum strains isolated from spoiled bakery products, was quantified. A full factorial design was set up for each strain. Data were collected at levels of a w varying from 0.80 to 0.98 and temperature from 15 to 35°C. Experiments were performed on malt agar, at pH5.5. When growth was observed, ca 20 individual growth kinetics per condition were recorded up to 35days. Radius of the colony vs time was then fitted with the Buchanan primary model. For each experimental condition, a lag time variability was observed, it was characterized by its mean, standard deviation (sd) and 5 th percentile, after a Normal distribution fit. As the environmental conditions became stressful (e.g. storage temperature and a w lower), mean and sd of single spore lag time distribution increased, indicating longer lag times and higher variability. The relationship between mean and sd followed a monotonous but not linear pattern, identical whatever the species. Next, secondary models were deployed to estimate the cardinal values (minimal, optimal and maximal temperatures, minimal water activity where no growth is observed anymore) for the three species. That enabled to confirm the observation made based on raw data analysis: concerning the temperature effect, A. niger behaviour was significantly different from E. repens and P. corylophilum: T opt of 37.4°C (standard deviation 1.4°C) instead of 27.1°C (1.4°C) and 25.2°C (1.2°C), respectively. Concerning the a w effect, from the three mould species, E. repens was the species able to grow at the lowest a w (aw min estimated to 0.74 (0.02)). Finally, results obtained with single spores were compared to findings from a previous study carried out at the population level (Dagnas et al., 2014). For short lag times (≤5days), there was no difference between lag

  6. The action of chemical and mechanical stresses on single and dual species biofilm removal of drinking water bacteria.

    Science.gov (United States)

    Gomes, I B; Lemos, M; Mathieu, L; Simões, M; Simões, L C

    2018-08-01

    The presence of biofilms in drinking water distribution systems (DWDS) is a global public health concern as they can harbor pathogenic microorganisms. Sodium hypochlorite (NaOCl) is the most commonly used disinfectant for microbial growth control in DWDS. However, its effect on biofilm removal is still unclear. This work aims to evaluate the effects of the combination of chemical (NaOCl) and mechanical stresses on the removal of single and dual species biofilms of two bacteria isolated from DWDS and considered opportunistic, Acinectobacter calcoaceticus and Stenotrophomonas maltophilia. A rotating cylinder reactor was successfully used for the first time in drinking water biofilm studies with polyvinyl chloride as substratum. The single and dual species biofilms presented different characteristics in terms of metabolic activity, mass, density, thickness and content of proteins and polysaccharides. Their complete removal was not achieved even when a high NaOCl concentrations and an increasing series of shear stresses (from 2 to 23Pa) were applied. In general, NaOCl pre-treatment did not improve the impact of mechanical stress on biofilm removal. Dual species biofilms were colonized mostly by S. maltophilia and were more susceptible to chemical and mechanical stresses than these single species. The most efficient treatment (93% biofilm removal) was the combination of NaOCl at 175mg·l -1 with mechanical stress against dual species biofilms. Of concern was the high tolerance of S. maltophilia to chemical and mechanical stresses in both single and dual species biofilms. The overall results demonstrate the inefficacy of NaOCl on biofilm removal even when combined with high shear stresses. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Viability of the Alaskan breeding population of Steller’s eiders

    Science.gov (United States)

    Dunham, Kylee; Grand, James B.

    2016-10-11

    The U.S. Fish and Wildlife Service is tasked with setting objective and measurable criteria for delisting species or populations listed under the Endangered Species Act. Determining the acceptable threshold for extinction risk for any species or population is a challenging task, particularly when facing marked uncertainty. The Alaskan breeding population of Steller’s eiders (Polysticta stelleri) was listed as threatened under the Endangered Species Act in 1997 because of a perceived decline in abundance throughout their nesting range and geographic isolation from the Russian breeding population. Previous genetic studies and modeling efforts, however, suggest that there may be dispersal from the Russian breeding population. Additionally, evidence exists of population level nonbreeding events. Research was conducted to estimate population viability of the Alaskan breeding population of Steller’s eiders, using both an open and closed model of population process for this threatened population. Projections under a closed population model suggest this population has a 100 percent probability of extinction within 42 years. Projections under an open population model suggest that with immigration there is no probability of permanent extinction. Because of random immigration process and nonbreeding behavior, however, it is likely that this population will continue to be present in low and highly variable numbers on the breeding grounds in Alaska. Monitoring the winter population, which includes both Russian and Alaskan breeding birds, may offer a more comprehensive indication of population viability.

  8. Redescription of the Advertisement Call of Five Species of Thoropa (Anura, Cycloramphidae, Including Recordings of Rare and Endangered Species.

    Directory of Open Access Journals (Sweden)

    Carlos H L Nunes-de-Almeida

    Full Text Available Frogs of the genus Thoropa comprise six endemic Brazilian species on the Eastern side of the country. Little is known about their natural history, especially about their acoustic communication. Therefore, aiming to provide an overview of their vocalizations, we analyzed and redescribed male advertisement calls of three living and two possibly extinct species. The smaller species, T. petropolitana and T. lutzi, produce simple calls (one single note with a higher frequency range than the remaining larger ones. On the other hand, the larger species present complex calls, with more than one note: T. megatympanum calls have three notes, T. taophora calls have four notes, and T. miliaris calls varies from three to six notes. Population snout-vent length negatively correlated with peak of dominant frequency as expected. However, highlighted differences between two populations of T. lutzi, which could indicate need of further taxonomic evaluation of those lineages. Peculiar morphology, such as the absence of vocal sacs and slits, may have contributed to their call variation and highly banded frequency structure. If the observed population differences reflect species-level differences, T. lutzi may be classified as a critically endangered species, as T. petropolitana. Furthermore, we provided a suggestion to an unusual behavior in frogs: calling with the mouth open in the smaller species of the genus.

  9. Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission.

    Directory of Open Access Journals (Sweden)

    Monica K Borucki

    2013-11-01

    Full Text Available One of the hurdles to understanding the role of viral quasispecies in RNA virus cross-species transmission (CST events is the need to analyze a densely sampled outbreak using deep sequencing in order to measure the amount of mutation occurring on a small time scale. In 2009, the California Department of Public Health reported a dramatic increase (350 in the number of gray foxes infected with a rabies virus variant for which striped skunks serve as a reservoir host in Humboldt County. To better understand the evolution of rabies, deep-sequencing was applied to 40 unpassaged rabies virus samples from the Humboldt outbreak. For each sample, approximately 11 kb of the 12 kb genome was amplified and sequenced using the Illumina platform. Average coverage was 17,448 and this allowed characterization of the rabies virus population present in each sample at unprecedented depths. Phylogenetic analysis of the consensus sequence data demonstrated that samples clustered according to date (1995 vs. 2009 and geographic location (northern vs. southern. A single amino acid change in the G protein distinguished a subset of northern foxes from a haplotype present in both foxes and skunks, suggesting this mutation may have played a role in the observed increased transmission among foxes in this region. Deep-sequencing data indicated that many genetic changes associated with the CST event occurred prior to 2009 since several nonsynonymous mutations that were present in the consensus sequences of skunk and fox rabies samples obtained from 20032010 were present at the sub-consensus level (as rare variants in the viral population in skunk and fox samples from 1995. These results suggest that analysis of rare variants within a viral population may yield clues to ancestral genomes and identify rare variants that have the potential to be selected for if environment conditions change.

  10. Energetic and ecological constraints on population density of reef fishes.

    Science.gov (United States)

    Barneche, D R; Kulbicki, M; Floeter, S R; Friedlander, A M; Allen, A P

    2016-01-27

    Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction. © 2016 The Author(s).

  11. Movement patterns for a critically endangered species, the leatherback turtle (Dermochelys coriacea, linked to foraging success and population status.

    Directory of Open Access Journals (Sweden)

    Helen Bailey

    Full Text Available Foraging success for pelagic vertebrates may be revealed by horizontal and vertical movement patterns. We show markedly different patterns for leatherback turtles in the North Atlantic versus Eastern Pacific, which feed on gelatinous zooplankton that are only occasionally found in high densities. In the Atlantic, travel speed was characterized by two modes, indicative of high foraging success at low speeds (<15 km d(-1 and transit at high speeds (20-45 km d(-1. Only a single mode was evident in the Pacific, which occurred at speeds of 21 km d(-1 indicative of transit. The mean dive depth was more variable in relation to latitude but closer to the mean annual depth of the thermocline and nutricline for North Atlantic than Eastern Pacific turtles. The most parsimonious explanation for these findings is that Eastern Pacific turtles rarely achieve high foraging success. This is the first support for foraging behaviour differences between populations of this critically endangered species and suggests that longer periods searching for prey may be hindering population recovery in the Pacific while aiding population maintenance in the Atlantic.

  12. Host and parasite life history interplay to yield divergent population genetic structures in two ectoparasites living on the same bat species.

    Science.gov (United States)

    van Schaik, J; Dekeukeleire, D; Kerth, G

    2015-05-01

    Host-parasite interactions are ubiquitous in nature. However, how parasite population genetic structure is shaped by the interaction between host and parasite life history remains understudied. Studies comparing multiple parasites infecting a single host can be used to investigate how different parasite life history traits interplay with host behaviour and life history. In this study, we used 10 newly developed microsatellite loci to investigate the genetic structure of a parasitic bat fly (Basilia nana). Its host, the Bechstein's bat (Myotis bechsteinii), has a social system and roosting behaviour that restrict opportunities for parasite transmission. We compared fly genetic structure to that of the host and another parasite, the wing-mite, Spinturnix bechsteini. We found little spatial or temporal genetic structure in B. nana, suggesting a large, stable population with frequent genetic exchange between fly populations from different bat colonies. This contrasts sharply with the genetic structure of the wing-mite, which is highly substructured between the same bat colonies as well as temporally unstable. Our results suggest that although host and parasite life history interact to yield similar transmission patterns in both parasite species, the level of gene flow and eventual spatiotemporal genetic stability is differentially affected. This can be explained by the differences in generation time and winter survival between the flies and wing-mites. Our study thus exemplifies that the population genetic structure of parasites on a single host can vary strongly as a result of how their individual life history characteristics interact with host behaviour and life history traits. © 2015 John Wiley & Sons Ltd.

  13. Evidence of population resistance to extreme low flows in a fluvial-dependent fish species

    Science.gov (United States)

    Katz, Rachel A.; Freeman, Mary C.

    2015-01-01

    Extreme low streamflows are natural disturbances to aquatic populations. Species in naturally intermittent streams display adaptations that enhance persistence during extreme events; however, the fate of populations in perennial streams during unprecedented low-flow periods is not well-understood. Biota requiring swift-flowing habitats may be especially vulnerable to flow reductions. We estimated the abundance and local survival of a native fluvial-dependent fish species (Etheostoma inscriptum) across 5 years encompassing historic low flows in a sixth-order southeastern USA perennial river. Based on capturemark-recapture data, the study shoal may have acted as a refuge during severe drought, with increased young-of-the-year (YOY) recruitment and occasionally high adult immigration. Contrary to expectations, summer and autumn survival rates (30 days) were not strongly depressed during low-flow periods, despite 25%-80% reductions in monthly discharge. Instead, YOY survival increased with lower minimum discharge and in response to small rain events that increased low-flow variability. Age-1+ fish showed the opposite pattern, with survival decreasing in response to increasing low-flow variability. Results from this population dynamics study of a small fish in a perennial river suggest that fluvial-dependent species can be resistant to extreme flow reductions through enhanced YOY recruitment and high survival

  14. Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.

    Science.gov (United States)

    Ingram, Colleen M; Troendle, Nicholas J; Gill, Clare A; Braude, Stanton; Honeycutt, Rodney L

    2015-10-01

    The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole-rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as a mating system) are the driving forces for the evolution of this eusocial species. One caveat to accepting this long-held view is that the original genetic studies were based on limited sampling from the species' geographic distribution. A growing body of evidence supports a contrary view, with the original samples not representative of the species-rather reflecting a single founder event, establishing a small population south of the Athi River. Our study is the first to address these competing hypotheses by examining patterns of molecular variation in colonies sampled from north and south of the Athi and Tana rivers, which based on our results, serve to isolate genetically distinct populations of naked mole-rats. Although colonies south of the Athi River share a single mtDNA haplotype and are fixed at most microsatellite loci, populations north of the Athi River are considerably more variable. Our findings support the position that the low variation observed in naked mole-rat populations south of the Athi River reflects a founder event, rather than a consequence of this species' unusual mating system. © 2015 John Wiley & Sons Ltd.

  15. Glacial history of a modern invader: phylogeography and species distribution modelling of the Asian tiger mosquito Aedes albopictus.

    Directory of Open Access Journals (Sweden)

    Daniele Porretta

    Full Text Available BACKGROUND: The tiger mosquito, Aedes albopictus, is one of the 100 most invasive species in the world and a vector of human diseases. In the last 30 years, it has spread from its native range in East Asia to Africa, Europe, and the Americas. Although this modern invasion has been the focus of many studies, the history of the species' native populations remains poorly understood. Here, we aimed to assess the role of Pleistocene climatic changes in shaping the current distribution of the species in its native range. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the phylogeography, historical demography, and species distribution of Ae. albopictus native populations at the Last Glacial Maximum (LGM. Individuals from 16 localities from East Asia were analyzed for sequence variation at two mitochondrial genes. No phylogeographic structure was observed across the study area. Demographic analyses showed a signature of population expansion that started roughly 70,000 years BP. The occurrence of a continuous and climatically suitable area comprising Southeast China, Indochinese Peninsula, and Sundaland during LGM was indicated by species distribution modelling. CONCLUSIONS/SIGNIFICANCE: Our results suggest an evolutionary scenario in which, during the last glacial phase, Ae. albopictus did not experience a fragmentation phase but rather persisted in interconnected populations and experienced demographic growth. The wide ecological flexibility of the species probably played a crucial role in its response to glacial-induced environmental changes. Currently, there is little information on the impact of Pleistocene climatic changes on animal species in East Asia. Most of the studies focused on forest-associated species and suggested cycles of glacial fragmentation and post-glacial expansion. The case of Ae. albopictus, which exhibits a pattern not previously observed in the study area, adds an important piece to our understanding of the Pleistocene history

  16. Species distribution model transferability and model grain size - finer may not always be better.

    Science.gov (United States)

    Manzoor, Syed Amir; Griffiths, Geoffrey; Lukac, Martin

    2018-05-08

    Species distribution models have been used to predict the distribution of invasive species for conservation planning. Understanding spatial transferability of niche predictions is critical to promote species-habitat conservation and forecasting areas vulnerable to invasion. Grain size of predictor variables is an important factor affecting the accuracy and transferability of species distribution models. Choice of grain size is often dependent on the type of predictor variables used and the selection of predictors sometimes rely on data availability. This study employed the MAXENT species distribution model to investigate the effect of the grain size on model transferability for an invasive plant species. We modelled the distribution of Rhododendron ponticum in Wales, U.K. and tested model performance and transferability by varying grain size (50 m, 300 m, and 1 km). MAXENT-based models are sensitive to grain size and selection of variables. We found that over-reliance on the commonly used bioclimatic variables may lead to less accurate models as it often compromises the finer grain size of biophysical variables which may be more important determinants of species distribution at small spatial scales. Model accuracy is likely to increase with decreasing grain size. However, successful model transferability may require optimization of model grain size.

  17. Diffusion of multiple species with excluded-volume effects

    KAUST Repository

    Bruna, Maria; Chapman, S. Jonathan

    2012-01-01

    Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results. © 2012 American Institute of Physics.

  18. Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia.

    Science.gov (United States)

    DeBiasse, Melissa B; Hellberg, Michael E

    2015-02-01

    Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.

  19. Model-Based Evaluation of Urban River Restoration: Conflicts between Sensitive Fish Species and Recreational Users

    Directory of Open Access Journals (Sweden)

    Aude Zingraff-Hamed

    2018-05-01

    Full Text Available Urban rivers are socioecological systems, and restored habitats may be attractive to both sensitive species and recreationists. Understanding the potential conflicts between ecological and recreational values is a critical issue for the development of a sustainable river-management plan. Habitat models are very promising tools for the ecological evaluation of river restoration projects that are already concluded, ongoing, or even to be planned. With our paper, we make a first attempt at integrating recreational user pressure into habitat modeling. The objective of this study was to analyze whether human impact is likely to hinder the re-establishment of a target species despite the successful restoration of physical habitat structures in the case of the restoration of the Isar River in Munich (Germany and the target fish species Chondostroma nasus L. Our analysis combined high-resolution 2D hydrodynamic modeling with mapping of recreational pressure and used an expert-based procedure for modeling habitat suitability. The results are twofold: (1 the restored river contains suitable physical habitats for population conservation but has low suitability for recruitment; (2 densely used areas match highly suitable habitats for C. nasus. In the future, the integrated modeling procedure presented here may allow ecological refuge for sensitive target species to be included in the design of restoration and may help in the development of visitor-management plans to safeguard biodiversity and recreational ecosystem services.

  20. Species invasion shifts the importance of predator dependence.

    Science.gov (United States)

    Griffen, Blaine D; Delaney, David G

    2007-12-01

    The strength of interference between foraging individuals can influence per capita consumption rates, with important consequences for predator and prey populations and system stability. Here we demonstrate how the replacement of a previously established invader, the predatory crab Carcinus maenas, by the recently invading predatory crab Hemigrapsus sanguineus shifts predation from a species that experiences strong predator interference (strong predator dependence) to one that experiences weak predator interference (weak predator dependence). We demonstrate using field experiments that differences in the strength of predator dependence persist for these species both when they forage on a single focal prey species only (the mussel Mytilus edulis) and when they forage more broadly across the entire prey community. This shift in predator dependence with species replacement may be altering the biomass across trophic levels, consistent with theoretical predictions, as we show that H. sanguineus populations are much larger than C. maenas populations throughout their invaded ranges. Our study highlights that predator dependence may differ among predator species and demonstrates that different predatory impacts of two conspicuous invasive predators may be explained at least in part by different strengths of predator dependence.

  1. Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

    Science.gov (United States)

    Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

    2015-01-01

    Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

  2. Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

    Science.gov (United States)

    Franklin, J.; Wejnert, K.E.; Hathaway, S.A.; Rochester, C.J.; Fisher, R.N.

    2009-01-01

    Aim: Several studies have found that more accurate predictive models of species' occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species' survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location: Coastal southern California, USA. Methods: Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver-operating characteristic (ROC) plot based on twofold cross-validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results: Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions: Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the

  3. Multi-population genomic prediction using a multi-task Bayesian learning model.

    Science.gov (United States)

    Chen, Liuhong; Li, Changxi; Miller, Stephen; Schenkel, Flavio

    2014-05-03

    Genomic prediction in multiple populations can be viewed as a multi-task learning problem where tasks are to derive prediction equations for each population and multi-task learning property can be improved by sharing information across populations. The goal of this study was to develop a multi-task Bayesian learning model for multi-population genomic prediction with a strategy to effectively share information across populations. Simulation studies and real data from Holstein and Ayrshire dairy breeds with phenotypes on five milk production traits were used to evaluate the proposed multi-task Bayesian learning model and compare with a single-task model and a simple data pooling method. A multi-task Bayesian learning model was proposed for multi-population genomic prediction. Information was shared across populations through a common set of latent indicator variables while SNP effects were allowed to vary in different populations. Both simulation studies and real data analysis showed the effectiveness of the multi-task model in improving genomic prediction accuracy for the smaller Ayshire breed. Simulation studies suggested that the multi-task model was most effective when the number of QTL was small (n = 20), with an increase of accuracy by up to 0.09 when QTL effects were lowly correlated between two populations (ρ = 0.2), and up to 0.16 when QTL effects were highly correlated (ρ = 0.8). When QTL genotypes were included for training and validation, the improvements were 0.16 and 0.22, respectively, for scenarios of the low and high correlation of QTL effects between two populations. When the number of QTL was large (n = 200), improvement was small with a maximum of 0.02 when QTL genotypes were not included for genomic prediction. Reduction in accuracy was observed for the simple pooling method when the number of QTL was small and correlation of QTL effects between the two populations was low. For the real data, the multi-task model achieved an

  4. Genome-wide single nucleotide polymorphisms (SNPs) for a model invasive ascidian Botryllus schlosseri.

    Science.gov (United States)

    Gao, Yangchun; Li, Shiguo; Zhan, Aibin

    2018-04-01

    Invasive species cause huge damages to ecology, environment and economy globally. The comprehensive understanding of invasion mechanisms, particularly genetic bases of micro-evolutionary processes responsible for invasion success, is essential for reducing potential damages caused by invasive species. The golden star tunicate, Botryllus schlosseri, has become a model species in invasion biology, mainly owing to its high invasiveness nature and small well-sequenced genome. However, the genome-wide genetic markers have not been well developed in this highly invasive species, thus limiting the comprehensive understanding of genetic mechanisms of invasion success. Using restriction site-associated DNA (RAD) tag sequencing, here we developed a high-quality resource of 14,119 out of 158,821 SNPs for B. schlosseri. These SNPs were relatively evenly distributed at each chromosome. SNP annotations showed that the majority of SNPs (63.20%) were located at intergenic regions, and 21.51% and 14.58% were located at introns and exons, respectively. In addition, the potential use of the developed SNPs for population genomics studies was primarily assessed, such as the estimate of observed heterozygosity (H O ), expected heterozygosity (H E ), nucleotide diversity (π), Wright's inbreeding coefficient (F IS ) and effective population size (Ne). Our developed SNP resource would provide future studies the genome-wide genetic markers for genetic and genomic investigations, such as genetic bases of micro-evolutionary processes responsible for invasion success.

  5. Population genetics models of local ancestry.

    Science.gov (United States)

    Gravel, Simon

    2012-06-01

    Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population structure and gene flow and interpret genomes of individuals that have ancestry from multiple source populations as mosaics of segments originating from each population. This article describes general and tractable models for local ancestry patterns with a focus on the length distribution of continuous ancestry tracts and the variance in total ancestry proportions among individuals. The models offer improved agreement with Wright-Fisher simulation data when compared to the state-of-the art and can be used to infer time-dependent migration rates from multiple populations. Considering HapMap African-American (ASW) data, we find that a model with two distinct phases of "European" gene flow significantly improves the modeling of both tract lengths and ancestry variances.

  6. Is the climate right for pleistocene rewilding? Using species distribution models to extrapolate climatic suitability for mammals across continents.

    Directory of Open Access Journals (Sweden)

    Orien M W Richmond

    Full Text Available Species distribution models (SDMs are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial "Pleistocene rewilding" proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of

  7. A hierarchical integrated population model for greater sage-grouse (Centrocercus urophasianus) in the Bi-State Distinct Population Segment, California and Nevada

    Science.gov (United States)

    Coates, Peter S.; Halstead, Brian J.; Blomberg, Erik J.; Brussee, Brianne; Howe, Kristy B.; Wiechman, Lief; Tebbenkamp, Joel; Reese, Kerry P.; Gardner, Scott C.; Casazza, Michael L.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus, hereafter referred to as “sage-grouse”) are endemic to sagebrush (Artemisia spp.) ecosystems throughout Western North America. Populations of sage-grouse have declined in distribution and abundance across the range of the species (Schroeder and others, 2004; Knick and Connelly, 2011), largely as a result of human disruption of sagebrush communities (Knick and Connelly, 2011). The Bi-State Distinct Population Segment (DPS) represents sage-grouse populations that are geographically isolated and genetically distinct (Benedict and others, 2003; Oyler-McCance and others, 2005) and that are present at the extreme southwestern distribution of the sage-grouse range (Schroeder and others, 2004), straddling the border of California and Nevada. Subpopulations of sage-grouse in the DPS may be at increased risk of extirpation because of a substantial loss of sagebrush habitat and lack of connectivity (Oyler-McCance and others, 2005). Sage-grouse in the Bi-State DPS represent small, localized breeding populations distributed across 18,325 km2. The U.S. Fish and Wildlife Service currently (2014) is evaluating the Bi-State DPS as threatened or endangered under the Endangered Species Act of 1973, independent of other sage-grouse populations. This DPS was designated as a higher priority for listing than sage-grouse in other parts of the species’ range (U.S. Department of the Interior, 2010). Range-wide population analyses for sage-grouse have included portions of the Bi-State DPS (Sage and Columbian Sharp-tailed Grouse Technical Committee 2008; Garton and others, 2011). Although these analyses are informative, the underlying data only represent a portion of the DPS and are comprised of lek count observations only. A thorough examination of population dynamics and persistence that includes multiple subpopulations and represents the majority of the DPS is largely lacking. Furthermore, fundamental information on population growth

  8. Integrated population modeling of black bears in Minnesota: implications for monitoring and management.

    Directory of Open Access Journals (Sweden)

    John R Fieberg

    Full Text Available BACKGROUND: Wildlife populations are difficult to monitor directly because of costs and logistical challenges associated with collecting informative abundance data from live animals. By contrast, data on harvested individuals (e.g., age and sex are often readily available. Increasingly, integrated population models are used for natural resource management because they synthesize various relevant data into a single analysis. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the performance of integrated population models applied to black bears (Ursus americanus in Minnesota, USA. Models were constructed using sex-specific age-at-harvest matrices (1980-2008, data on hunting effort and natural food supplies (which affects hunting success, and statewide mark-recapture estimates of abundance (1991, 1997, 2002. We compared this approach to Downing reconstruction, a commonly used population monitoring method that utilizes only age-at-harvest data. We first conducted a large-scale simulation study, in which our integrated models provided more accurate estimates of population trends than did Downing reconstruction. Estimates of trends were robust to various forms of model misspecification, including incorrectly specified cub and yearling survival parameters, age-related reporting biases in harvest data, and unmodeled temporal variability in survival and harvest rates. When applied to actual data on Minnesota black bears, the model predicted that harvest rates were negatively correlated with food availability and positively correlated with hunting effort, consistent with independent telemetry data. With no direct data on fertility, the model also correctly predicted 2-point cycles in cub production. Model-derived estimates of abundance for the most recent years provided a reasonable match to an empirical population estimate obtained after modeling efforts were completed. CONCLUSIONS/SIGNIFICANCE: Integrated population modeling provided a reasonable

  9. Population genetics of the potentially invasive African fruit fly species, Ceratitis rosa and Ceratitis fasciventris (Diptera: Tephritidae).

    Science.gov (United States)

    Baliraine, F N; Bonizzoni, M; Guglielmino, C R; Osir, E O; Lux, S A; Mulaa, F J; Gomulski, L M; Zheng, L; Quilici, S; Gasperi, G; Malacrida, A R

    2004-03-01

    A set of 10 microsatellite markers was used to survey the levels of genetic variability and to analyse the genetic aspects of the population dynamics of two potentially invasive pest fruit fly species, Ceratitis rosa and C. fasciventris, in Africa. The loci were derived from the closely related species, C. capitata. The degree of microsatellite polymorphism in C. rosa and C. fasciventris was extensive and comparable to that of C. capitata. In C. rosa, the evolution of microsatellite polymorphism in its distribution area reflects the colonization history of this species. The mainland populations are more polymorphic than the island populations. Low levels of differentiation were found within the Africa mainland area, while greater levels of differentiation affect the islands. Ceratitis fasciventris is a central-east African species. The microsatellite data over the Uganda/Kenya spatial scale suggest a recent expansion and possibly continuing gene flow within this area. The microsatellite variability data from C. rosa and C. fasciventris, together with those of C. capitata, support the hypothesis of an east African origin of the Ceratitis spp.

  10. Adoption of parasitic Maculinea alcon caterpillars (Lepidoptera : Lycaenidae) by three Myrmica ant species

    DEFF Research Database (Denmark)

    Als, Thomas Damm; Nash, David Richard; Boomsma, J. J.

    2001-01-01

    Maculinea butterflies are parasites of Myrmica ant nests. The Alcon blue, Maculinea alcon, is unusual in that it parasitizes the nests of several Myrmica species, using M. rubra, M. ruginodis and M. scabrinodis as hosts in different parts of Europe. In Denmark it uses M. rubra and M. ruginodis....... alcon from three populations differing in their host use to laboratory nests of all three recorded host ant species collected from each of the M. alcon populations. We measured the attractiveness of the caterpillars to their host ants as the time taken for them to be adopted by each ant colony....... Caterpillars from all populations took longer to be adopted to M. scabrinodis nests than to nests of the other two ant species. Adoption times to M. rubra and M. ruginodis colonies differed: caterpillars from each of the two populations that used a single host species were adopted most quickly by that species...

  11. Comparison of explicit and effective models for calculating ionic populations in argon plasmas

    International Nuclear Information System (INIS)

    Abdallah, J. Jr.; Clark, R.E.H.

    1994-01-01

    Calculations have been performed to model the state populations of argon plasmas at electron densities at and above those required for the validity of coronal equilibrium. Both effective and explicit models have been used, and both are based on the same set of atomic cross sections. The effective model includes ground and singly excited states explicitly, while the effect of autoionizing states is accounted for by branching factors which describe their depopulation into the various non-autoionizing states. The explicit model considers both autoionizing and non-autoionizing states explicitly. The effective model requires a significantly reduced amount of computer time and memory. Good agreement between the two models can be obtained through moderate densities if the branching factors include electron density dependent terms which describe the collisional stabilization of each autoionizing state. The effective model breaks down as density is increased because the population of individual autoionizing states become significant. Results for both ionization balance and radiated power loss are presented. (Author)

  12. The temporal spectrum of adult mosquito population fluctuations: conceptual and modeling implications.

    Directory of Open Access Journals (Sweden)

    Yun Jian

    Full Text Available An improved understanding of mosquito population dynamics under natural environmental forcing requires adequate field observations spanning the full range of temporal scales over which mosquito abundance fluctuates in natural conditions. Here we analyze a 9-year daily time series of uninterrupted observations of adult mosquito abundance for multiple mosquito species in North Carolina to identify characteristic scales of temporal variability, the processes generating them, and the representativeness of observations at different sampling resolutions. We focus in particular on Aedes vexans and Culiseta melanura and, using a combination of spectral analysis and modeling, we find significant population fluctuations with characteristic periodicity between 2 days and several years. Population dynamical modelling suggests that the observed fast fluctuations scales (2 days-weeks are importantly affected by a varying mosquito activity in response to rapid changes in meteorological conditions, a process neglected in most representations of mosquito population dynamics. We further suggest that the range of time scales over which adult mosquito population variability takes place can be divided into three main parts. At small time scales (indicatively 2 days-1 month observed population fluctuations are mainly driven by behavioral responses to rapid changes in weather conditions. At intermediate scales (1 to several month environmentally-forced fluctuations in generation times, mortality rates, and density dependence determine the population characteristic response times. At longer scales (annual to multi-annual mosquito populations follow seasonal and inter-annual environmental changes. We conclude that observations of adult mosquito populations should be based on a sub-weekly sampling frequency and that predictive models of mosquito abundance must include behavioral dynamics to separate the effects of a varying mosquito activity from actual changes in the

  13. A simple model for skewed species-lifetime distributions

    KAUST Repository

    Murase, Yohsuke; Shimada, Takashi; Ito, Nobuyasu

    2010-01-01

    A simple model of a biological community assembly is studied. Communities are assembled by successive migrations and extinctions of species. In the model, species are interacting with each other. The intensity of the interaction between each pair

  14. Species Distribution Modeling: Comparison of Fixed and Mixed Effects Models Using INLA

    Directory of Open Access Journals (Sweden)

    Lara Dutra Silva

    2017-12-01

    Full Text Available Invasive alien species are among the most important, least controlled, and least reversible of human impacts on the world’s ecosystems, with negative consequences affecting biodiversity and socioeconomic systems. Species distribution models have become a fundamental tool in assessing the potential spread of invasive species in face of their native counterparts. In this study we compared two different modeling techniques: (i fixed effects models accounting for the effect of ecogeographical variables (EGVs; and (ii mixed effects models including also a Gaussian random field (GRF to model spatial correlation (Matérn covariance function. To estimate the potential distribution of Pittosporum undulatum and Morella faya (respectively, invasive and native trees, we used geo-referenced data of their distribution in Pico and São Miguel islands (Azores and topographic, climatic and land use EGVs. Fixed effects models run with maximum likelihood or the INLA (Integrated Nested Laplace Approximation approach provided very similar results, even when reducing the size of the presences data set. The addition of the GRF increased model adjustment (lower Deviance Information Criterion, particularly for the less abundant tree, M. faya. However, the random field parameters were clearly affected by sample size and species distribution pattern. A high degree of spatial autocorrelation was found and should be taken into account when modeling species distribution.

  15. A centroid model of species distribution with applications to the Carolina wren Thryothorus ludovicianus and house finch Haemorhous mexicanus in the United States

    Science.gov (United States)

    Huang, Qiongyu; Sauer, John R.; Swatantran, Anu; Dubayah, Ralph

    2016-01-01

    Drastic shifts in species distributions are a cause of concern for ecologists. Such shifts pose great threat to biodiversity especially under unprecedented anthropogenic and natural disturbances. Many studies have documented recent shifts in species distributions. However, most of these studies are limited to regional scales, and do not consider the abundance structure within species ranges. Developing methods to detect systematic changes in species distributions over their full ranges is critical for understanding the impact of changing environments and for successful conservation planning. Here, we demonstrate a centroid model for range-wide analysis of distribution shifts using the North American Breeding Bird Survey. The centroid model is based on a hierarchical Bayesian framework which models population change within physiographic strata while accounting for several factors affecting species detectability. Yearly abundance-weighted range centroids are estimated. As case studies, we derive annual centroids for the Carolina wren and house finch in their ranges in the U.S. We further evaluate the first-difference correlation between species’ centroid movement and changes in winter severity, total population abundance. We also examined associations of change in centroids from sub-ranges. Change in full-range centroid movements of Carolina wren significantly correlate with snow cover days (r = −0.58). For both species, the full-range centroid shifts also have strong correlation with total abundance (r = 0.65, and 0.51 respectively). The movements of the full-range centroids of the two species are correlated strongly (up to r = 0.76) with that of the sub-ranges with more drastic population changes. Our study demonstrates the usefulness of centroids for analyzing distribution changes in a two-dimensional spatial context. Particularly it highlights applications that associate the centroid with factors such as environmental stressors, population characteristics

  16. Bias correction in species distribution models: pooling survey and collection data for multiple species.

    Science.gov (United States)

    Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A

    2015-04-01

    Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence-absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence-absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model's performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence-absence data for a given species is scarceIf we have only presence-only data and no presence-absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species' geographic range.

  17. Constructing stage-structured matrix population models from life tables: comparison of methods

    Directory of Open Access Journals (Sweden)

    Masami Fujiwara

    2017-10-01

    Full Text Available A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates of a population and can be used for calculating an asymptotic finite population growth rate (λ and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used

  18. Single and multispecies reference points for Baltic fish stocks

    DEFF Research Database (Denmark)

    Gislason, Henrik

    1999-01-01

    reference points. Management advice based on biomass reference points will also differ. In the single species situation the combinations of cod and pelagic fishing effort for which the equilibrium spawning- stock biomass of the three species is above the biomass reference points forms a rectangular area......Single and multispecies models are used to examine the effect of species interaction on biological reference points for cod, herring, and sprat in the Baltic. The results demonstrate that reference points are different in single and multispecies contexts. Reference points for fishing mortality...... based on single-species yield and SSB calculations are difficult to use when natural mortality depends on the absolute abundance of the predators and their alternative prey. Reference points based on maximizing total yield from the system may lead to impractical results when species interact...

  19. Anthropogenic disturbances affect population size and biomass allocation of two alpine species from the headwater area of the Urumqi River, China

    International Nuclear Information System (INIS)

    Zhao, R.; Zhang, H.; An, L.

    2018-01-01

    The survival of alpine plants are seriously threatened by increasing anthropogenic activity. Saussurea involucrata and Rhodiola quadrifida are particularly affected because of their high medicinal value. To assess the impact of anthropogenic disturbance on the two species, their population size and biomass allocation were examined at three levels of disturbance at low and high altitudes. Anthropogenic disturbance was the most serious threat to the populations and changed the population density, biomass, and biomass allocation of both species significantly (p<0.05). The changes differed with the species and the altitude, and were also affected by the interaction between these two factors. Population density and biomass of the two species decreased with an increase in the level of anthropogenic disturbance. These results imply that the decrease in population size and in biomass allocation to reproductive organs due to anthropogenic disturbances may make the plant populations even smaller and scarce. Meanwhile, change of making their survival dependent on the extent of anthropogenic disturbance: unless such disturbance is checked and the species are protected, they will probably disappear from the headwater area of the Urumqi River. This influence of anthropogenic disturbances may be potential threats to population ability of survival and reproduction. (author)

  20. Population genetic structure of Brazilian shrimp species (Farfantepenaeus sp., F. brasiliensis, F. paulensis and Litopenaeus schmitti: Decapoda: Penaeidae

    Directory of Open Access Journals (Sweden)

    Jaqueline Gusmão

    2005-03-01

    Full Text Available Penaeid shrimps are important resources for worldwide fisheries and aquaculture. In the Southwest Atlantic, Farfantepenaeus brasiliensis, F. paulensis, F. subtilis, Farfantepenaeus sp. and Litopenaeus schmitti are among the most important commercially exploited species. Despite their high commercial value, there is little information available on the different aspects of their biology or genetics and almost no data on their stock structure. We used allozymes to estimate variability levels and population genetic structure of F. brasiliensis, F. paulensis, L. schmitti and the recently detected species Farfantepenaeus sp. along as much as 4,000 km of Brazilian coastline. No population heterogeneity was detected in F. brasiliensis or L. schmitti along the studied area. In contrast, F ST values found for Farfantepenaeus sp. and F. paulensis indicate that the populations of those two species are genetically structured, comprising different fishery stocks. The largest genetic differences in F. paulensis were found between Lagoa dos Patos (South and the two populations from Southeast Brazil. In Farfantepenaeus sp., significant differences were detected between the population from Recife and those from Fortaleza and Ilhéus.

  1. Molecular Population Genetics.

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-03-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

  2. Mathematical Modeling of Extinction of Inhomogeneous Populations

    Science.gov (United States)

    Karev, G.P.; Kareva, I.

    2016-01-01

    Mathematical models of population extinction have a variety of applications in such areas as ecology, paleontology and conservation biology. Here we propose and investigate two types of sub-exponential models of population extinction. Unlike the more traditional exponential models, the life duration of sub-exponential models is finite. In the first model, the population is assumed to be composed clones that are independent from each other. In the second model, we assume that the size of the population as a whole decreases according to the sub-exponential equation. We then investigate the “unobserved heterogeneity”, i.e. the underlying inhomogeneous population model, and calculate the distribution of frequencies of clones for both models. We show that the dynamics of frequencies in the first model is governed by the principle of minimum of Tsallis information loss. In the second model, the notion of “internal population time” is proposed; with respect to the internal time, the dynamics of frequencies is governed by the principle of minimum of Shannon information loss. The results of this analysis show that the principle of minimum of information loss is the underlying law for the evolution of a broad class of models of population extinction. Finally, we propose a possible application of this modeling framework to mechanisms underlying time perception. PMID:27090117

  3. Do we need demographic data to forecast plant population dynamics?

    Science.gov (United States)

    Tredennick, Andrew T.; Hooten, Mevin B.; Adler, Peter B.

    2017-01-01

    Rapid environmental change has generated growing interest in forecasts of future population trajectories. Traditional population models built with detailed demographic observations from one study site can address the impacts of environmental change at particular locations, but are difficult to scale up to the landscape and regional scales relevant to management decisions. An alternative is to build models using population-level data that are much easier to collect over broad spatial scales than individual-level data. However, it is unknown whether models built using population-level data adequately capture the effects of density-dependence and environmental forcing that are necessary to generate skillful forecasts.Here, we test the consequences of aggregating individual responses when forecasting the population states (percent cover) and trajectories of four perennial grass species in a semi-arid grassland in Montana, USA. We parameterized two population models for each species, one based on individual-level data (survival, growth and recruitment) and one on population-level data (percent cover), and compared their forecasting accuracy and forecast horizons with and without the inclusion of climate covariates. For both models, we used Bayesian ridge regression to weight the influence of climate covariates for optimal prediction.In the absence of climate effects, we found no significant difference between the forecast accuracy of models based on individual-level data and models based on population-level data. Climate effects were weak, but increased forecast accuracy for two species. Increases in accuracy with climate covariates were similar between model types.In our case study, percent cover models generated forecasts as accurate as those from a demographic model. For the goal of forecasting, models based on aggregated individual-level data may offer a practical alternative to data-intensive demographic models. Long time series of percent cover data already exist

  4. Population Density Modeling for Diverse Land Use Classes: Creating a National Dasymetric Worker Population Model

    Science.gov (United States)

    Trombley, N.; Weber, E.; Moehl, J.

    2017-12-01

    Many studies invoke dasymetric mapping to make more accurate depictions of population distribution by spatially restricting populations to inhabited/inhabitable portions of observational units (e.g., census blocks) and/or by varying population density among different land classes. LandScan USA uses this approach by restricting particular population components (such as residents or workers) to building area detected from remotely sensed imagery, but also goes a step further by classifying each cell of building area in accordance with ancillary land use information from national parcel data (CoreLogic, Inc.'s ParcelPoint database). Modeling population density according to land use is critical. For instance, office buildings would have a higher density of workers than warehouses even though the latter would likely have more cells of detection. This paper presents a modeling approach by which different land uses are assigned different densities to more accurately distribute populations within them. For parts of the country where the parcel data is insufficient, an alternate methodology is developed that uses National Land Cover Database (NLCD) data to define the land use type of building detection. Furthermore, LiDAR data is incorporated for many of the largest cities across the US, allowing the independent variables to be updated from two-dimensional building detection area to total building floor space. In the end, four different regression models are created to explain the effect of different land uses on worker distribution: A two-dimensional model using land use types from the parcel data A three-dimensional model using land use types from the parcel data A two-dimensional model using land use types from the NLCD data, and A three-dimensional model using land use types from the NLCD data. By and large, the resultant coefficients followed intuition, but importantly allow the relationships between different land uses to be quantified. For instance, in the model

  5. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

    Science.gov (United States)

    Allman, Elizabeth S; Degnan, James H; Rhodes, John A

    2011-06-01

    Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

  6. Assessing combined impacts of agrochemicals: Aquatic macroinvertebrate population responses in outdoor mesocosms.

    Science.gov (United States)

    Barmentlo, S Henrik; Schrama, Maarten; Hunting, Ellard R; Heutink, Roel; van Bodegom, Peter M; de Snoo, Geert R; Vijver, Martina G

    2018-08-01

    Agricultural ditches host a diverse community of species. These species often are unwarrantedly exposed to fertilizers and a wide-array of pesticides (hereafter: agrochemicals). Standardized ecotoxicological research provides valuable information to predict whether these pesticides possibly pose a threat to the organisms living within these ditches, in particular macro-invertebrates. However, knowledge on how mixtures of these agrochemicals affect macro-invertebrates under realistic abiotic conditions and with population and community complexity is mostly lacking. Therefore we examined here, using a full factorial design, the population responses of macroinvertebrate species assemblages exposed to environmentally relevant concentrations of three commonly used agrochemicals (for 35days) in an outdoor experiment. The agrochemicals selected were an insecticide (imidacloprid), herbicide (terbuthylazine) and nutrients (NPK), all having a widespread usage and often detected together in watersheds. Effects on species abundance and body length caused by binary mixture combinations could be described from single substance exposure. However, when agrochemicals were applied as tertiary mixtures, as they are commonly found in agricultural waters, species' abundance often deviated from expectations made based on the three single treatments. This indicates that pesticide-mixture induced toxicity to population relevant endpoints are difficult to extrapolate to field conditions. As in agricultural ditches often a multitude (approx. up to 7) of agrochemicals residues are detected, we call other scientist to verify the ecological complexity of non-additive induced shifts in natural aquatic invertebrate populations and aquatic species assemblages. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. High population variability and source-sink dynamics in a solitary bee species.

    Science.gov (United States)

    Franzén, Markus; Nilsson, Sven G

    2013-06-01

    Although solitary bees are considered to play key roles in ecosystem functions, surprisingly few studies have explored their population dynamics. We investigated the population dynamics of a rare, declining, solitary bee (Andrena humilis) in a landscape of 80 km2 in southern Sweden from 2003 to 2011. Only one population was persistent throughout all years studied; most likely this population supplied the surrounding landscape with 11 smaller, temporary local populations. Despite stable pollen availability, the size of the persistent population fluctuated dramatically in a two-year cycle over the nine years, with 490-1230 nests in odd-numbered years and 21-48 nests in even-numbered years. These fluctuations were not significantly related to climatic variables or pollen availability. Nineteen colonization and 14 extinction events were recorded. Occupancy decreased with distance from the persistent population and increased with increasing resource (pollen) availability. There were significant positive correlations between the size of the persistent population and patch occupancy and colonization. Colonizations were generally more common in patches closer to the persistent population, whereas extinctions were independent of distance from the persistent population. Our results highlight the complex population dynamics that exist for this solitary bee species, which could be due to source-sink dynamics, a prolonged diapause, or can represent a bet-hedging strategy to avoid natural enemies and survive in small habitat patches. If large fluctuations in solitary bee populations prove to be widespread, it will have important implications for interpreting ecological relationships, bee conservation, and pollination.

  8. Predictive thermodynamic models for liquid--liquid extraction of single, binary and ternary lanthanides and actinides

    International Nuclear Information System (INIS)

    Hoh, Y.C.

    1977-03-01

    Chemically based thermodynamic models to predict the distribution coefficients and the separation factors for the liquid--liquid extraction of lanthanides-organophosphorus compounds were developed by assuming that the quotient of the activity coefficients of each species varies slightly with its concentrations, by using aqueous lanthanide or actinide complexes stoichiometric stability constants expressed as its degrees of formation, by making use of the extraction mechanism and the equilibrium constant for the extraction reaction. For a single component system, the thermodynamic model equations which predict the distribution coefficients, are dependent on the free organic concentration, the equilibrated ligand and hydrogen ion concentrations, the degree of formation, and on the extraction mechanism. For a binary component system, the thermodynamic model equation which predicts the separation factors is the same for all cases. This model equation is dependent on the degrees of formation of each species in their binary system and can be used in a ternary component system to predict the separation factors for the solutes relative to each other

  9. Long-term impacts of selective logging on two Amazonian tree species with contrasting ecological and reproductive characteristics: inferences from Eco-gene model simulations.

    Science.gov (United States)

    Vinson, C C; Kanashiro, M; Sebbenn, A M; Williams, T C R; Harris, S A; Boshier, D H

    2015-08-01

    The impact of logging and subsequent recovery after logging is predicted to vary depending on specific life history traits of the logged species. The Eco-gene simulation model was used to evaluate the long-term impacts of selective logging over 300 years on two contrasting Brazilian Amazon tree species, Dipteryx odorata and Jacaranda copaia. D. odorata (Leguminosae), a slow growing climax tree, occurs at very low densities, whereas J. copaia (Bignoniaceae) is a fast growing pioneer tree that occurs at high densities. Microsatellite multilocus genotypes of the pre-logging populations were used as data inputs for the Eco-gene model and post-logging genetic data was used to verify the output from the simulations. Overall, under current Brazilian forest management regulations, there were neither short nor long-term impacts on J. copaia. By contrast, D. odorata cannot be sustainably logged under current regulations, a sustainable scenario was achieved by increasing the minimum cutting diameter at breast height from 50 to 100 cm over 30-year logging cycles. Genetic parameters were only slightly affected by selective logging, with reductions in the numbers of alleles and single genotypes. In the short term, the loss of alleles seen in J. copaia simulations was the same as in real data, whereas fewer alleles were lost in D. odorata simulations than in the field. The different impacts and periods of recovery for each species support the idea that ecological and genetic information are essential at species, ecological guild or reproductive group levels to help derive sustainable management scenarios for tropical forests.

  10. Inter-island transfers and population dynamics of Seychelles Warblers Acrocephalus sechellensis

    NARCIS (Netherlands)

    Komdeur, Jan

    1997-01-01

    In the 1950s the Seychelles Warbler Acrocephalus sechellensis was a highly threatened single-island endemic species with a population of 26 individuals confined to Cousin Island in the inner Seychelles. Following long-term management of Cousin, the population steadily recovered to around 300–360

  11. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    Thomas E Gorochowski

    Full Text Available Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

  12. Proximal Soil Sensing - A Contribution for Species Habitat Distribution Modelling of Earthworms in Agricultural Soils?

    Science.gov (United States)

    Schirrmann, Michael; Joschko, Monika; Gebbers, Robin; Kramer, Eckart; Zörner, Mirjam; Barkusky, Dietmar; Timmer, Jens

    2016-01-01

    Earthworms are important for maintaining soil ecosystem functioning and serve as indicators of soil fertility. However, detection of earthworms is time-consuming, which hinders the assessment of earthworm abundances with high sampling density over entire fields. Recent developments of mobile terrestrial sensor platforms for proximal soil sensing (PSS) provided new tools for collecting dense spatial information of soils using various sensing principles. Yet, the potential of PSS for assessing earthworm habitats is largely unexplored. This study investigates whether PSS data contribute to the spatial prediction of earthworm abundances in species distribution models of agricultural soils. Proximal soil sensing data, e.g., soil electrical conductivity (EC), pH, and near infrared absorbance (NIR), were collected in real-time in a field with two management strategies (reduced tillage / conventional tillage) and sandy to loam soils. PSS was related to observations from a long-term (11 years) earthworm observation study conducted at 42 plots. Earthworms were sampled from 0.5 x 0.5 x 0.2 m³ soil blocks and identified to species level. Sensor data were highly correlated with earthworm abundances observed in reduced tillage but less correlated with earthworm abundances observed in conventional tillage. This may indicate that management influences the sensor-earthworm relationship. Generalized additive models and state-space models showed that modelling based on data fusion from EC, pH, and NIR sensors produced better results than modelling without sensor data or data from just a single sensor. Regarding the individual earthworm species, particular sensor combinations were more appropriate than others due to the different habitat requirements of the earthworms. Earthworm species with soil-specific habitat preferences were spatially predicted with higher accuracy by PSS than more ubiquitous species. Our findings suggest that PSS contributes to the spatial modelling of

  13. Proximal Soil Sensing - A Contribution for Species Habitat Distribution Modelling of Earthworms in Agricultural Soils?

    Directory of Open Access Journals (Sweden)

    Michael Schirrmann

    Full Text Available Earthworms are important for maintaining soil ecosystem functioning and serve as indicators of soil fertility. However, detection of earthworms is time-consuming, which hinders the assessment of earthworm abundances with high sampling density over entire fields. Recent developments of mobile terrestrial sensor platforms for proximal soil sensing (PSS provided new tools for collecting dense spatial information of soils using various sensing principles. Yet, the potential of PSS for assessing earthworm habitats is largely unexplored. This study investigates whether PSS data contribute to the spatial prediction of earthworm abundances in species distribution models of agricultural soils.Proximal soil sensing data, e.g., soil electrical conductivity (EC, pH, and near infrared absorbance (NIR, were collected in real-time in a field with two management strategies (reduced tillage / conventional tillage and sandy to loam soils. PSS was related to observations from a long-term (11 years earthworm observation study conducted at 42 plots. Earthworms were sampled from 0.5 x 0.5 x 0.2 m³ soil blocks and identified to species level. Sensor data were highly correlated with earthworm abundances observed in reduced tillage but less correlated with earthworm abundances observed in conventional tillage. This may indicate that management influences the sensor-earthworm relationship. Generalized additive models and state-space models showed that modelling based on data fusion from EC, pH, and NIR sensors produced better results than modelling without sensor data or data from just a single sensor. Regarding the individual earthworm species, particular sensor combinations were more appropriate than others due to the different habitat requirements of the earthworms. Earthworm species with soil-specific habitat preferences were spatially predicted with higher accuracy by PSS than more ubiquitous species.Our findings suggest that PSS contributes to the spatial

  14. Population dynamics, antibiotics resistance and biofilm formation of Aeromonas and Vibrio species isolated from aquatic sources in Northern Malaysia.

    Science.gov (United States)

    Odeyemi, Olumide A; Ahmad, Asmat

    2017-02-01

    This study aimed to compare population dynamics, antibiotic resistance and biofilm formation of Aeromonas and Vibrio species from seawater and sediment collected from Northern Malaysia. Isolates with different colony morphology were characterized using both biochemical and molecular methods before testing for antibiotic resistance and biofilm formation. Results obtained from this study showed that in Kedah, the population of Aeromonas isolated from sediment was highest in Pantai Merdeka (8.22 log CFU/ml), Pulau Bunting recorded the highest population of Aeromonas from sediment (8.43 log CFU/g). It was observed that Vibrio species isolated from seawater and sediment were highest in Kuala Sanglang (9.21 log CFU/ml). In Kuala Perlis, the population of Aeromonas isolated from seawater was highest in Jeti (7.94 log CFU/ml). Highest population of Aeromonas from sediment was recorded in Kampong Tanah Baru (7.99 log CFU/g). It was observed that Vibrio species isolated from seawater was highest in Padang Benta (8.42 log CFU/g) while Jeti Kuala Perlis had highest population of Vibrio isolated from sediment. It was observed that location does not influence population of Aeromonas. The results of the independent t - test revealed that there was no significant relationship between location and population of Vibrio (df = 10, t = 1.144, p > 0.05). The occurrence of biofilm formation and prevalence of antibiotic resistant Aeromonas and Vibrio species in seawater and sediment pose danger to human and aquatic animals' health. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Spatial Complementarity and the Coexistence of Species

    Science.gov (United States)

    Velázquez, Jorge; Garrahan, Juan P.; Eichhorn, Markus P.

    2014-01-01

    Coexistence of apparently similar species remains an enduring paradox in ecology. Spatial structure has been predicted to enable coexistence even when population-level models predict competitive exclusion if it causes each species to limit its own population more than that of its competitor. Nevertheless, existing hypotheses conflict with regard to whether clustering favours or precludes coexistence. The spatial segregation hypothesis predicts that in clustered populations the frequency of intra-specific interactions will be increased, causing each species to be self-limiting. Alternatively, individuals of the same species might compete over greater distances, known as heteromyopia, breaking down clusters and opening space for a second species to invade. In this study we create an individual-based model in homogeneous two-dimensional space for two putative sessile species differing only in their demographic rates and the range and strength of their competitive interactions. We fully characterise the parameter space within which coexistence occurs beyond population-level predictions, thereby revealing a region of coexistence generated by a previously-unrecognised process which we term the triadic mechanism. Here coexistence occurs due to the ability of a second generation of offspring of the rarer species to escape competition from their ancestors. We diagnose the conditions under which each of three spatial coexistence mechanisms operates and their characteristic spatial signatures. Deriving insights from a novel metric — ecological pressure — we demonstrate that coexistence is not solely determined by features of the numerically-dominant species. This results in a common framework for predicting, given any pair of species and knowledge of the relevant parameters, whether they will coexist, the mechanism by which they will do so, and the resultant spatial pattern of the community. Spatial coexistence arises from complementary combinations of traits in each

  16. Induction of prophage lambda by chlorinated organics: Detection of some single-species/single-site carcinogens

    Energy Technology Data Exchange (ETDEWEB)

    DeMarini, D.M.; Brooks, H.G. (Environmental Protection Agency, Research Triangle Park, NC (United States))

    1992-01-01

    Twenty-eight chlorinated organic compounds were evaluated for their ability to induce DNA damage using the Microscreen prophage-induction assay in Escherichia coli. Comparison of the performance characteristics of the prophage-induction and Salmonella assays to rodent carcinogenicity assays showed that the prophage-induction assay had a somewhat higher specificity than did the Salmonella assay (70% vs. 50%); sensitivity, concordance, and positive and negative predictivity were similar for the two microbial assays. The Microscreen prophage-induction assay failed to detect eight carcinogens, perhaps due to toxicity or other unknown factors; five of these eight carcinogens were detected by the Salmonella assay. However, the prophage-induction assay did detect six carcinogens that were not detected by the Salmonella assay, and five of these were single-species, single-site carcinogens, mostly mouse liver carcinogens. Some of these carcinogens, such as the chloroethanes, produce free radicals, which may be the basis for their carcinogenicity and ability to induce prophage. The prophage-induction (or other SOS) assay may be useful in identifying some genotoxic chlorinated carcinogens that induce DNA damage that do not revert the standard Salmonella tester strains.

  17. Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

    Science.gov (United States)

    Pyne, Robert M; Honig, Josh A; Vaiciunas, Jennifer; Wyenandt, Christian A; Simon, James E

    2018-04-23

    The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure

  18. An open-population hierarchical distance sampling model

    Science.gov (United States)

    Sollmann, Rachel; Beth Gardner,; Richard B Chandler,; Royle, J. Andrew; T Scott Sillett,

    2015-01-01

    Modeling population dynamics while accounting for imperfect detection is essential to monitoring programs. Distance sampling allows estimating population size while accounting for imperfect detection, but existing methods do not allow for direct estimation of demographic parameters. We develop a model that uses temporal correlation in abundance arising from underlying population dynamics to estimate demographic parameters from repeated distance sampling surveys. Using a simulation study motivated by designing a monitoring program for island scrub-jays (Aphelocoma insularis), we investigated the power of this model to detect population trends. We generated temporally autocorrelated abundance and distance sampling data over six surveys, using population rates of change of 0.95 and 0.90. We fit the data generating Markovian model and a mis-specified model with a log-linear time effect on abundance, and derived post hoc trend estimates from a model estimating abundance for each survey separately. We performed these analyses for varying number of survey points. Power to detect population changes was consistently greater under the Markov model than under the alternatives, particularly for reduced numbers of survey points. The model can readily be extended to more complex demographic processes than considered in our simulations. This novel framework can be widely adopted for wildlife population monitoring.

  19. An open-population hierarchical distance sampling model.

    Science.gov (United States)

    Sollmann, Rahel; Gardner, Beth; Chandler, Richard B; Royle, J Andrew; Sillett, T Scott

    2015-02-01

    Modeling population dynamics while accounting for imperfect detection is essential to monitoring programs. Distance sampling allows estimating population size while accounting for imperfect detection, but existing methods do not allow for estimation of demographic parameters. We develop a model that uses temporal correlation in abundance arising from underlying population dynamics to estimate demographic parameters from repeated distance sampling surveys. Using a simulation study motivated by designing a monitoring program for Island Scrub-Jays (Aphelocoma insularis), we investigated the power of this model to detect population trends. We generated temporally autocorrelated abundance and distance sampling data over six surveys, using population rates of change of 0.95 and 0.90. We fit the data generating Markovian model and a mis-specified model with a log-linear time effect on abundance, and derived post hoc trend estimates from a model estimating abundance for each survey separately. We performed these analyses for varying numbers of survey points. Power to detect population changes was consistently greater under the Markov model than under the alternatives, particularly for reduced numbers of survey points. The model can readily be extended to more complex demographic processes than considered in our simulations. This novel framework can be widely adopted for wildlife population monitoring.

  20. Modelling future oil production, population and the economy

    Energy Technology Data Exchange (ETDEWEB)

    Laherrere, Jean

    2003-07-01

    Most published data on energy, population and the economy are unreliable. In many cases, authors have political motives, selectively choosing data from a wide range of uncertainty to give a desired image. In addition to the uncertainty of the measurements themselves, as in the case of population or the confidentiality of the oil reserves, they often indulge in manipulation. A so-called hedonistic factor distorts the calculation of GDP in the United States; and the definition of the Proved Reserves by the Securities and Exchange Commission gives rise to 'reserve growth'. OPEC misreports its oil reserves because its quotas depend upon the reported reserves, and the reserves were overestimated in the Soviet Union because economic and technical constraints were ignored. Our present culture of eternal growth makes the word 'decline' politically incorrect, but constant growth is unsustainable in a finite world. Growth is the Santa Claus of the modern age who is supposed to provide welfare and retirement for our children and us. All natural events, when measured over their full life, can be modelled under one or more cycles, as in the Fourier analysis. This cyclical nature corresponds with the finite nature of the Universe; everything that is born will die, whether we speak of the solar system, the Earth, or human species. What goes up must come down. The Russian population is already declining and Europe's will soon do so too. This basic understanding was recognised by the celebrated King Hubbert when he made his famous prediction in 1956 that US oil production would peak in 1970. But, in fact, he oversimplified by showing a single peak. In reality, US oil production had a secondary peak (93% of the first one) in 1985, reflecting the entry of Alaskan production, which itself peaked in 1988. A symmetrical oil cycle reflects a large number of independent producers, acting randomly, but in many cases economic and political factors disturb the